From e1819fdd39c25c45716f35544e0f69fa7dafa566 Mon Sep 17 00:00:00 2001 From: Zane Selvans Date: Mon, 13 Nov 2023 10:01:41 -0600 Subject: [PATCH] * Rename tox-pytest and update-lockfile workflows. * Make scheduled PRs against dev rather than conda-lockfile branch. * Update docs to reflect swapping Make in for Tox. * Update to pyarrow 14 and grpcio 1.59 b/c security --- .github/workflows/bot-auto-merge.yml | 2 +- .../workflows/{tox-pytest.yml => pytest.yml} | 2 +- ...lockfile.yml => update-conda-lockfile.yml} | 8 +- MANIFEST.in | 14 - Makefile | 5 +- README.rst | 18 +- docs/conf.py | 1 - docs/dev/annual_updates.rst | 36 +- docs/dev/build_docs.rst | 8 +- docs/dev/dev_setup.rst | 132 +- docs/dev/nightly_data_builds.rst | 2 +- docs/dev/project_management.rst | 40 +- docs/dev/pudl_id_mapping.rst | 25 +- docs/dev/testing.rst | 265 +-- environments/conda-linux-64.lock.yml | 61 +- environments/conda-lock.yml | 1628 +++++++++++------ environments/conda-osx-64.lock.yml | 59 +- environments/conda-osx-arm64.lock.yml | 59 +- pyproject.toml | 8 +- tox.ini | 250 --- 20 files changed, 1388 insertions(+), 1235 deletions(-) rename .github/workflows/{tox-pytest.yml => pytest.yml} (99%) rename .github/workflows/{update-lockfile.yml => update-conda-lockfile.yml} (91%) delete mode 100644 MANIFEST.in delete mode 100644 tox.ini diff --git a/.github/workflows/bot-auto-merge.yml b/.github/workflows/bot-auto-merge.yml index 56f5fbb6eb..898775e50a 100644 --- a/.github/workflows/bot-auto-merge.yml +++ b/.github/workflows/bot-auto-merge.yml @@ -4,7 +4,7 @@ name: bot-auto-merge on: workflow_run: types: [completed] - workflows: ["tox-pytest"] + workflows: ["pytest"] jobs: bot-auto-merge: diff --git a/.github/workflows/tox-pytest.yml b/.github/workflows/pytest.yml similarity index 99% rename from .github/workflows/tox-pytest.yml rename to .github/workflows/pytest.yml index 7956b0cf51..b808b84c42 100644 --- a/.github/workflows/tox-pytest.yml +++ b/.github/workflows/pytest.yml @@ -1,5 +1,5 @@ --- -name: tox-pytest +name: pytest on: pull_request: diff --git a/.github/workflows/update-lockfile.yml b/.github/workflows/update-conda-lockfile.yml similarity index 91% rename from .github/workflows/update-lockfile.yml rename to .github/workflows/update-conda-lockfile.yml index 24081b3b49..21a839f727 100644 --- a/.github/workflows/update-lockfile.yml +++ b/.github/workflows/update-conda-lockfile.yml @@ -1,5 +1,5 @@ --- -name: update-lockfile +name: update-conda-lockfile on: workflow_dispatch: @@ -9,7 +9,7 @@ on: paths: - "pyproject.toml" - "environments/*" - - ".github/workflows/update-lockfile.yml" + - ".github/workflows/update-conda-lockfile.yml" # What branch does this action run on? # - workflow_dispatch: Whatever branch it was run against. @@ -31,7 +31,7 @@ jobs: - name: Set GITHUB_REF for use with schedule if: ${{ (github.event_name == 'schedule') }} run: | - echo "GITHUB_REF=conda-lockfile" >> $GITHUB_ENV + echo "GITHUB_REF=dev" >> $GITHUB_ENV - name: Set GITHUB_REF for use with push if: ${{ (github.event_name == 'push') }} run: | @@ -75,7 +75,7 @@ jobs: title: Update Lockfile body: > This pull request relocks the dependencies with conda-lock. - It is triggered by [update-lockfile](https://github.com/catalyst-cooperative/pudl/blob/main/.github/workflows/update-lockfile.yml). + It is triggered by [update-conda-lockfile](https://github.com/catalyst-cooperative/pudl/blob/main/.github/workflows/update-conda-lockfile.yml). labels: dependencies, conda-lock reviewers: zaneselvans branch: update-conda-lockfile diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 94feda81ec..0000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,14 +0,0 @@ -graft src/pudl/metadata/templates -graft src/pudl/output/sql - -prune .github -prune devtools -prune docker -prune docs -prune notebooks -prune terraform - -global-exclude .gitignore .gitattributes .git-blame-ignore-revs -global-exclude .bandit.yml .codecov.yml .coveragerc .mypy.ini -global-exclude .pre-commit-config.yaml .readthedocs.yaml -global-exclude docker-compose.yml diff --git a/Makefile b/Makefile index 21ca1e6583..172e3e9651 100644 --- a/Makefile +++ b/Makefile @@ -52,6 +52,7 @@ conda-lock.yml: pyproject.toml # Create the pudl-dev conda environment based on the universal lockfile .PHONY: pudl-dev pudl-dev: conda-lock.yml + ${mamba} run --name base ${mamba} env remove --name pudl-dev conda-lock install --name pudl-dev --${mamba} --dev environments/conda-lock.yml .PHONY: install-pudl @@ -123,12 +124,12 @@ pytest-coverage: coverage-erase docs-build pytest-unit pytest-integration .PHONY: pytest-integration-full pytest-integration-full: - pytest ${pytest_args} --etl-settings ${etl_full_yml} test/integration + pytest ${pytest_args} -n auto --live-dbs --etl-settings ${etl_full_yml} test/integration .PHONY: pytest-validate pytest-validate: - pytest --live-dbs test/validate pudl_check_fks + pytest ${pytest_args} -n auto --live-dbs test/validate # Run the full ETL, generating new FERC & PUDL SQLite DBs and EPA CEMS Parquet files. # Then run the full integration tests and data validations on all years of data. diff --git a/README.rst b/README.rst index df5edcda3e..8eea0e93b4 100644 --- a/README.rst +++ b/README.rst @@ -8,9 +8,9 @@ The Public Utility Data Liberation Project (PUDL) :target: https://www.repostatus.org/#active :alt: Project Status: Active -.. image:: https://github.com/catalyst-cooperative/pudl/workflows/tox-pytest/badge.svg - :target: https://github.com/catalyst-cooperative/pudl/actions?query=workflow%3Atox-pytest - :alt: Tox-PyTest Status +.. image:: https://github.com/catalyst-cooperative/pudl/workflows/pytest/badge.svg + :target: https://github.com/catalyst-cooperative/pudl/actions?query=workflow%3Apytest + :alt: PyTest Status .. image:: https://img.shields.io/codecov/c/github/catalyst-cooperative/pudl?style=flat&logo=codecov :target: https://codecov.io/gh/catalyst-cooperative/pudl @@ -20,18 +20,6 @@ The Public Utility Data Liberation Project (PUDL) :target: https://catalystcoop-pudl.readthedocs.io/en/latest/ :alt: Read the Docs Build Status -.. image:: https://img.shields.io/pypi/v/catalystcoop.pudl - :target: https://pypi.org/project/catalystcoop.pudl/ - :alt: PyPI Latest Version - -.. image:: https://img.shields.io/conda/vn/conda-forge/catalystcoop.pudl - :target: https://anaconda.org/conda-forge/catalystcoop.pudl - :alt: conda-forge Version - -.. image:: https://img.shields.io/pypi/pyversions/catalystcoop.pudl - :target: https://pypi.org/project/catalystcoop.pudl/ - :alt: Supported Python Versions - .. image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black :alt: Any color you want, so long as it's black. diff --git a/docs/conf.py b/docs/conf.py index b7d217c852..4b63dd1eb1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -91,7 +91,6 @@ "setuptools": ("https://setuptools.pypa.io/en/latest/", None), "sklearn": ("https://scikit-learn.org/stable", None), "sqlalchemy": ("https://docs.sqlalchemy.org/en/latest/", None), - "tox": ("https://tox.wiki/en/latest/", None), } # Add any paths that contain templates here, relative to this directory. diff --git a/docs/dev/annual_updates.rst b/docs/dev/annual_updates.rst index 57bbf13cbf..bc076d4d7b 100644 --- a/docs/dev/annual_updates.rst +++ b/docs/dev/annual_updates.rst @@ -321,9 +321,9 @@ A. FERC 1 & EIA Plants & Utilities :doc:`pudl_id_mapping` page for further instructions. -.. code-block:: bash +.. code-block:: console - tox -e get_unmapped_ids + $ make unmapped-ids .. note:: @@ -369,21 +369,21 @@ called from within the :class:`pudl.output.pudltabl.PudlTabl` class. * Are there new columns that should incorporated into the output tables? * Are there new tables that need to have an output function defined for them? -**8.2)** To ensure that you (more) fully exercise all of the possible output functions, -run the entire CI test suite against your live databases with: +**8.2)** To ensure that you fully exercise all of the possible output functions, +run all the integration tests against your live PUDL DB with: -.. code-block:: bash +.. code-block:: console - tox -e full -- --live-dbs + $ make pytest-integration-full 9. Run and Update Data Validations ----------------------------------- **9.1)** When the CI tests are passing against all years of data, sanity check the data in the database and the derived outputs by running -.. code-block:: bash +.. code-block:: console - tox -e validate + $ make pytest-validate We expect at least some of the validation tests to fail initially because we haven't updated the number of records we expect to see in each table. @@ -398,18 +398,18 @@ attention to how far off of previous expectations the new tables are. E.g. if th are already 20 years of data, and you're integrating 1 new year of data, probably the number of rows in the tables should be increasing by around 5% (since 1/20 = 0.05). -10. Run Additional Standalone Analyses --------------------------------------- -**10.1)** Run any important analyses that haven't been integrated into the CI -tests on the new year of data for sanity checking. For example the -:mod:`pudl.analysis.state_demand` script or generating the EIA Plant Parts List for -integration with FERC 1 data. - -11. Update the Documentation +10. Update the Documentation ---------------------------- -**11.1)** Once the new year of data is integrated, update the documentation -to reflect the new state of affairs. This will include updating at least: +**10.1)** Once the new year of data is integrated, update the documentation to reflect +the new state of affairs. This will include updating at least: * the top-level :doc:`README ` +* the :doc:`data access ` page * the :doc:`/release_notes` * any updated :doc:`data sources ` + +Check that the docs still build with + +.. code-block:: console + + $ make docs-build diff --git a/docs/dev/build_docs.rst b/docs/dev/build_docs.rst index d7f6f1b2da..9f15b13274 100644 --- a/docs/dev/build_docs.rst +++ b/docs/dev/build_docs.rst @@ -12,12 +12,12 @@ controlled by ``docs/conf.py``. If you are editing the documentation and need to regenerate the outputs as you go to see your changes reflected locally, the most reliable option is to -use Tox. Tox will remove the previously generated outputs and regenerate +use ``make``. Make will remove the previously generated outputs and regenerate everything from scratch: .. code-block:: console - $ tox -e docs + $ make docs-build If you're just working on a single page and don't care about the entire set of documents being regenerated and linked together, you can call Sphinx @@ -44,5 +44,5 @@ documentation in your text editor with appropriate plugins. need to be checked in to version control. Similarly the :doc:`../data_dictionaries/pudl_db` is generated dynamically - by the :mod:`pudl.convert.metadata_to_rst` script that gets run by Tox when - it builds the docs. + by the :mod:`pudl.convert.metadata_to_rst` script that gets run by Sphinx during + the docs build. diff --git a/docs/dev/dev_setup.rst b/docs/dev/dev_setup.rst index 183c5529c8..4e9caf339b 100644 --- a/docs/dev/dev_setup.rst +++ b/docs/dev/dev_setup.rst @@ -27,16 +27,13 @@ Linux) and are already familiar with ``git``, GitHub, and the Unix shell. * `Cloning a Repository `__ ------------------------------------------------------------------------------ -Install mambaforge +Install ``conda`` / ``mamba`` ------------------------------------------------------------------------------ -We use the ``mamba`` package manager to specify and update our development -environment, preferentially installing packages from the community maintained -`conda-forge `__ distribution channel. We recommend -using `mambaforge `__ rather than -it's ``conda`` equivalent -`miniconda `__ or the large pre-defined -collection of scientific packages bundled together in the Anaconda Python distribution -because it's faster. +We use the ``mamba`` package manager to specify and update our development environment, +preferentially installing packages from the community maintained `conda-forge +`__ distribution channel. We recommend using `miniforge +`__ to install ``mamba`` and automatically +default to the ``conda-forge`` channel. After installing your package manager, make sure it's configured to use `strict channel priority `__ @@ -47,6 +44,14 @@ with the following commands: $ mamba update mamba $ conda config --set channel_priority strict +At this point you should have a ``base`` ``conda`` environment. You'll need to install +``conda-lock`` to work with our environment lockfiles, discussed below: + +.. code-block:: console + + $ mamba activate base + $ mamba install conda-lock + ------------------------------------------------------------------------------ Fork and Clone the PUDL Repository ------------------------------------------------------------------------------ @@ -63,37 +68,87 @@ put it in a local directory where you can make changes. ------------------------------------------------------------------------------- Create the PUDL Dev Environment ------------------------------------------------------------------------------- -Inside the ``devtools`` directory of your newly cloned repository, you'll see an -``environment.yml`` file that specifies the ``pudl-dev`` ``conda`` environment. You can -create and activate that environment from within the main repository directory by -running: +We use `conda-lock `__ to specify particular +versions of all of PUDL's direct and indirect software dependencies in a lockfile, +resulting in a stable, reproducible environment. This lockfile and several +platform-specific rendered environment files are stored under the ``environments/`` +directory in the main PUDL repository. + +All of the dependencies in ``environments/conda-lock.yml`` are derived from packages +listed in the project's ``pyproject.toml`` file. The conda lockfile is updated +automatically by a GitHub Action workflow that runs once a week, or any time +``pyproject.toml`` is changed. + +Use ``conda-lock`` to create a new ``pudl-dev`` environment and activate it: .. code-block:: console - $ mamba update mamba - $ mamba env create --name pudl-dev --file devtools/environment.yml + $ mamba activate base + $ conda-lock install --name pudl-dev --mamba --dev environments/conda-lock.yml + $ mamba deactivate $ mamba activate pudl-dev -This environment installs the ``catalystcoop.pudl`` package directly using the code in -your cloned repository so that it can be edited during development. It also installs all -of the software PUDL depends on, some packages for testing and quality control, packages -for working with interactive Jupyter Notebooks, and a few Python packages that have -binary dependencies which can be easier to satisfy through ``conda`` packages. +Now we need to install the PUDL package defined by the repository into the ``pudl-dev`` +conda environment. We use ``pip`` since this is just a local package, and since all of +the required packages should have already been satisfied by the locked conda +environment, we tell ``pip`` not to try and install any dependencies. + +.. code-block:: console + + $ pip install --no-cache-dir --no-deps --editable . ------------------------------------------------------------------------------- -Updating the PUDL Dev Environment +Automating tasks with Make ------------------------------------------------------------------------------- -You will need to periodically update your development (``pudl-dev``) conda environment -to get you newer versions of existing dependencies and incorporate any changes to the -environment specification that have been made by other contributors. The most reliable -way to do this is to remove the existing environment and recreate it. +We use the GNU build tool ``make`` to remember and automate some repetitive tasks in the +PUDL repository, including creating and updating the ``pudl-dev`` conda environment. If +you are on a Unix-based platform (Linux or MacOS) it should already be installed. +Typically, rather than running the commands in the section above, you'll want to use +the predefined ``make`` commands. If you'd like to learn more about how Makefiles work, +check out `this excellent Makefile tutorial `__ + +To create the ``pudl-dev`` environment and install the local PUDL package, run: + +.. code-block:: console + + $ make install-pudl + +------------------------------------------------------------------------------- +Updating the PUDL Development Environment +------------------------------------------------------------------------------- + +You will need to periodically update your installed development (``pudl-dev``) conda +environment to get you newer versions of existing dependencies and incorporate any +changes to the environment specification that have been made by other contributors. The +most reliable way to do this is to remove the existing environment and recreate it. + +Recreating the ``pudl-dev`` environment from scratch uses the same ``make`` command as +creating it the first time: + +.. code-block:: console + + $ make install-pudl + +If you happen to be changing the dependencies listed in ``pyproject.toml`` and you want +to re-create the conda lockfile from scratch, resolving for any newly updated +dependencies, and then create a fresh ``pudl-dev`` environment using the new lockfile, +you can use: + +.. code-block:: console + + $ make conda-clean + $ make install-pudl + +However, unless you are adding or removing dependencies from ``pyproject.toml`` it is +probably best to just use the already prepared lockfile, and allow it to be updated +automatically by the weekly GitHub Action. .. note:: Different development branches within the repository may specify their own slightly different versions of the ``pudl-dev`` conda environment. As a result, you may need - to update your environment when switching from one branch to another. - + to update your environment when switching from one branch to another to ensure that + the codebase and the dependencies are in sync. If you want to work with the most recent version of the code on a branch named ``new-feature``, then from within the top directory of the PUDL repository you would do: @@ -102,10 +157,7 @@ If you want to work with the most recent version of the code on a branch named $ git checkout new-feature $ git pull - $ mamba deactivate - $ mamba update mamba - $ mamba env remove --name pudl-dev - $ mamba env create --name pudl-dev --file devtools/environment.yml + $ make install-pudl $ mamba activate pudl-dev If you are working with locally processed data and there have been changes to the @@ -176,12 +228,14 @@ If you are using an editor designed for Python development many of these code li and formatting tools can be run automatically in the background while you write code or documentation. Popular editors that work with the above tools include: -* `Visual Studio Code `__, from Microsoft (free) -* `Atom `__ developed by GitHub (free), and +* `Visual Studio Code `__, from Microsoft (free, but + controlled by the hegemon). +* `NeoVim `__, (free and open source; for diehard Unix lovers) +* `PyCharm `__ (paid). * `Sublime Text `__ (paid). Each of these editors have their own collection of plugins and settings for working -with linters and other code analysis tools. +with linters, formatters, and other code analysis tools. .. seealso:: @@ -311,12 +365,8 @@ The workspace is laid out like this: **Directory / File** **Contents** -------------------- ---------------------------------------------------------- ``data/`` Raw data, automatically organized by source, year, etc. - This is the path ``PUDL_INPUT`` can point to. --------------------- ---------------------------------------------------------- -``parquet/`` `Apache Parquet `__ files - generated by PUDL. --------------------- ---------------------------------------------------------- -``settings/`` Example configuration files for controlling PUDL scripts. + This is the path ``PUDL_INPUT`` should point to. -------------------- ---------------------------------------------------------- -``sqlite/`` :mod:`sqlite3` databases generated by PUDL. +``output/`` The directory into which all the durable products of the + PUDL data processing pipeline will be written. ==================== ========================================================== diff --git a/docs/dev/nightly_data_builds.rst b/docs/dev/nightly_data_builds.rst index 6de060f071..4ad3343e9d 100644 --- a/docs/dev/nightly_data_builds.rst +++ b/docs/dev/nightly_data_builds.rst @@ -21,7 +21,7 @@ are expected to pass. If they don't then someone needs to take responsibility fo getting them working again with some urgency. Because of how long the full build & tests take, we don’t typically run them -individually before merging every PR into ``dev``. However, running ``tox -e nuke`` +individually before merging every PR into ``dev``. However, running ``make nuke`` (the equivalent of the full builds) is recommended when you've added a new year of data or made other changes that would be expected to break the data validations, so that the appropriate changes can be made prior to those changes hitting ``dev`` and the nightly diff --git a/docs/dev/project_management.rst b/docs/dev/project_management.rst index cade805533..7041fad8dd 100644 --- a/docs/dev/project_management.rst +++ b/docs/dev/project_management.rst @@ -2,10 +2,10 @@ Project Management =============================================================================== -The people working on PUDL are distributed all over North America. -Collaboration takes place online. We make extensive use of Github's project -management tools as well as `Zenhub `__ which provides -additional features for sprint planning, task estimation, and progress reports. +The people working on PUDL are distributed all over North America. Collaboration takes +place online. We make extensive use of Github's build int project management tools and +we work in public. You can follow our progress in our +`GitHub Projects `__ ------------------------------------------------------------------------------- Issues and Project Tracking @@ -15,22 +15,20 @@ track bugs, enhancements, support requests, and just about any other work that g into the project. Try to make sure that issues have informative tags so we can find them easily. -We use Zenhub Sprints, Epics, and Releases to track our progress. These won't be -visible unless you have the `ZenHub browser extension -`__ installed. - ------------------------------------------------------------------------------- -GitHub Workflow +Our GitHub Workflow ------------------------------------------------------------------------------- + * We have 2 persistent branches: **main** and **dev**. * We create temporary feature branches off of **dev** and make pull requests to **dev** throughout our 2 week long sprints. -* At the end of each sprint, assuming all the tests are passing, **dev** is - merged into **main**. +* At the end of each sprint, or any time a particularly significant feature has + been merged in and the nightly builds are passing, **dev** is merged into **main**. ------------------------------------------------------------------------------- Pull Requests ------------------------------------------------------------------------------- + * Before making a PR, make sure the tests run and pass locally, including the code linters and pre-commit hooks. See :ref:`linting` for details. * Don't forget to merge any new commits to the **dev** branch into your feature @@ -52,12 +50,18 @@ Pull Requests ------------------------------------------------------------------------------- Releases ------------------------------------------------------------------------------- -* Periodically, we tag a new release on **main** and upload the packages to - the Python Package Index and `conda-forge `__. -* Whenever we tag a release on Github, the repository is archived on `Zenodo - `__ and issued a DOI. -* For some software releases we archive processed data on Zenodo along with a - Docker container that encapsulates the necessary software environment. + +* The PUDL data processing pipeline isn't intended to be used as a library that other + Python packages depend on. Rather, it's an end-use application that produces data + which other applications and analyses can consume. Because of this, we no longer + release installable packages on PyPI or ``conda-forge``. +* Periodically, we tag a versioned release on **main** using the date, like + ``v2023.07.15``. This triggers a snapshot of the repository being + `archived on Zenodo `__. +* The nightly build outputs associated with any tagged release will also get archived + `on Zenodo here `__ + and be made available longer term in the + `AWS Open Data Registry `__. ------------------------------------------------------------------------------- User Support @@ -65,4 +69,4 @@ User Support We don't (yet) have funding to do user support, so it's currently all community and volunteer based. In order to ensure that others can find the answers to questions that have already been asked, we try to do all support in public -using Github issues. +using `Github Discussions `__. diff --git a/docs/dev/pudl_id_mapping.rst b/docs/dev/pudl_id_mapping.rst index 7a2d80adb9..60f3381573 100644 --- a/docs/dev/pudl_id_mapping.rst +++ b/docs/dev/pudl_id_mapping.rst @@ -75,21 +75,24 @@ Checking for Unmapped Records ----------------------------- With every new year of data comes the possibility of new plants and utilities. Once -you’ve integrated the new data into PUDL :doc:`(see these instructions) -`, you’ll need to check for unmapped utility and plants. To do this, -run the glue tests with specific arguments, or directly run the following ``tox`` test. -This test identifies plants and utilities which exist in the updated FERC 1 and EIA -datasets that do not yet appear in the stored ID maps. This will generate a complete -databse based on the settings files stored in -``pudl/package_data/settings/etl_full.yml`` without foreign-key constraints and save -any unmapped IDs to the ``devtools/ferc1-eia-glue`` directory that correspond to -unmapped plants and utilities from FERC 1 and EIA. +you've integrated the new data into PUDL :doc:`(see instructions) `, +you'll need to check for unmapped utility and plants. To do this, +run the glue tests with specific arguments, or directly run the following ``make`` +command. .. code-block:: console - $ tox -e get_unmapped_ids + $ make unmapped_ids -If you have already generated a databse without foreign-key constraints, you can +This invokes a script that identifies plants and utilities which exist in the updated +FERC 1 and EIA datasets that do not yet appear in the stored ID maps. This will generate +a complete database based on the settings files stored in +``pudl/package_data/settings/etl_full.yml`` without foreign-key constraints and save any +unmapped IDs to the ``devtools/ferc1-eia-glue`` directory that correspond to unmapped +plants and utilities from FERC 1 and EIA. + +If you have already generated a databse without foreign-key constraints, you can run +just the script that extracts the umapped IDs with: .. code-block:: console diff --git a/docs/dev/testing.rst b/docs/dev/testing.rst index 6729ce11a0..18821ada2d 100644 --- a/docs/dev/testing.rst +++ b/docs/dev/testing.rst @@ -3,32 +3,24 @@ =============================================================================== Testing PUDL =============================================================================== -We use `Tox `__ to coordinate our software testing -and to manage other build and sanity checking tools. Under the hood, it invokes -a variety of other collections of command-line tools in predefined combinations -that are described in ``tox.ini``. These include software tests defined using -`pytest `__, code linters like ``ruff``, documentation -generators like Sphinx, and sanity checks defined as git pre-commit hooks. Each -of these tools, or sometimes collections of related tools, can be selected at -the command line. They can also be run independently without using Tox, but for -the sake of simplicitly and standardization, we try to mostly just run them -using the predefined settings we have configured in Tox. - -The simplest way to test PUDL -- which is also how the code is tested -automatically by our continuous integration setup -- is to just run Tox alone -with no arguments. This will typically take 25 minutes to run. +We use `pytest `__ to specify software unit & integration tests, +and to coordinate data validation tests. There are several ``pytest`` commands stored +as targets in the PUDL ``Makefile`` for convenience and to ensure that we're all running +the tests in similar ways by default. + +To run the software unit and integration tests that will be run in our automated CI on +GitHub, you can use the following command: .. code-block:: console - $ tox + $ make pytest-unit pytest-integration .. note:: - If you aren't familiar with pytest and Tox already, you may want to go - peruse their introductory documentation. + If you aren't familiar with pytest and Make already, you may want to check out: * `Getting Started with pytest `__ - * `Tox Documentation `__ + * `Makefile Tutorial `__ ------------------------------------------------------------------------------- Software Tests @@ -46,7 +38,8 @@ each with its own subdirectory: parts of the overall software system and in some cases interactions with external systems requiring network connectivity. The main thing our integration tests do is run the full PUDL data processing pipeline for the - most recent year of data. This takes around 15 minutes. + most recent year of data. Depending on your machine, this can take from 20 + minutes to an hour... or more. * **Data Validations** (``test/validate/``) sanity check the PUDL outputs generated by the data processing pipeline. This helps us catch issues with the input data as well as more subtle bugs that don't prevent the code from @@ -55,136 +48,47 @@ each with its own subdirectory: different from the other tests. ------------------------------------------------------------------------------- -Running tests with Tox +Running tests with Make ------------------------------------------------------------------------------- -Tox installs the PUDL package in a fresh Python environment, ensuring that the -tests only have access to packages which would be installed on a new user's -computer. Tox's overall behavior is configured with the ``tox.ini`` file in the -main repository directory. There are several different "test environments" -defined to test different aspects of the software or to perform other -actions like building the documentation. We'll go through some of the most -common ones below. - -Continuous Integration Tests -^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Our default tox test environment is ``ci`` -- that includes all of the tests -that will be run in continuous integration using a `GitHub Action -`__. You should run these tests before -pushing code to the repository or making a pull request. Because it's the -default test environment, it will be run if you call Tox without any -arguments: - -.. code-block:: console - - $ tox - -This is equivalent to: - -.. code-block:: console - - $ tox -e ci - -If the PUDL package's dependencies have been changed (in ``setup.py``) or you -recently ran the tests while on another branch of the repository with other -dependencies, you may need to tell Tox to recreate the software environment -it uses with the ``-r`` flag. This behavior is turned on by default for the -``ci``, ``full``, and ``validate`` tests since they take a long time to run -and the extra time required to recreate the software environment is short by -comparison. - -In addition to running the ``unit`` and ``integration`` tests, the CI test -environment lints the code and documentation input files and uses Sphinx to -build the documentation. It also generates a test coverage report. Running -the full set of CI tests takes 20-25 minutes and requires a fair amount of -data. If you don't already have that data downloaded, it will be downloaded -automatically and put in your :doc:`local datastore ` - -.. note:: - - Locally the tests will run using whatever version of Python is part of your - ``pudl-dev`` conda environment, but we have our CI set up to test on both - Python 3.8 and 3.9 in parallel. - -Software Unit and Integration Tests -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To run the ``unit`` or ``integration`` tests on their own, you use the ``-e`` -flag to choose those test environments explicitly: - -.. code-block:: console - - $ tox -e unit - -or: - -.. code-block:: console - $ tox -e integration - -Full ETL Tests -^^^^^^^^^^^^^^ -As mentioned above, the CI tests process a single year of data. If you would -like to more exhaustively test the ETL process without affecting your -existing FERC 1 and PUDL databases, you can use the ``full`` test -environment which may take close to an hour to run: - -.. code-block:: console - - $ tox -e full - -This will process *all years of data* for the EIA and FERC datasets and all -years of EPA CEMS data for a single state (Idaho). The ETL parameters for -this test are defined in ``test/settings/full-integration-tests.yml`` - - -Running Other Commands with Tox -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -You can run any of the individual test environments that ``tox -av`` lists on -their own: - -.. code-block:: console - - $ tox -av - - default environments: - ci -> Run all continuous integration (CI) checks & generate test coverage. - - additional environments: - ruff -> Run the ruff linter but without autofixes enabled. - pre_commit -> Run git pre-commit hooks not covered by the other linters. - linters -> Run the pre-commit and ruff linters. - doc8 -> Check the documentation input files for syntactical correctness. - docs -> Remove old docs output and rebuild HTML from scratch with Sphinx - unit -> Run all the software unit tests. - integration -> Run all software integration tests and process a full year of data. - minmax_rows -> Check that all outputs have the expected number of rows. - validate -> Run all data validation tests. This requires a complete PUDL DB. - jupyter -> Ensure that designated Jupyter notebooks can be executed. - full_integration -> Run ETL and integration tests for all years and data sources. - full -> Run all CI checks, but for all years of data. - nuke -> Nuke & recreate SQLite & Parquet outputs, then run all tests and - data validations against the new outputs. - get_unmapped_ids -> Make the raw FERC1 DB and generate a PUDL database with only EIA in - order to generate any unmapped IDs. - -Note that not all of them literally run tests. For instance, to lint and build the -documentation you can run: - -.. code-block:: console - - $ tox -e docs - -To run all of the code and documentation linters, but not run any of the other -tests: - -.. code-block:: console - - $ tox -e linters - -Each of the test environments defined in ``tox.ini`` is just a collection of -dependencies and commands. To see what they consist of, you can open the file -in your text editor. Each section starts with ``[testenv:xxxxxx]`` and the -section called ``commands`` is a list of shell commands that that test -environment will run. +The ``Makefile`` targets that pertain to software and data tests which are coordianted +by ``pytest`` are prefixed with ``pytest-`` + +In addition to running the ``pytest-unit`` and ``pytest-integration`` targets mentioned +above there are also: + +* ``pytest-validate``: The full data validation tests, which run on an already + existing PUDL DB. +* ``pytest-integration-full``: The integration tests, but run on all years of data + rather than just the most recent year. This test also assumes you already have a live + PUDL DB. +* ``pytest-jupyter``: Check that select Jupyter notebooks checked into the repository + can run successfully. (Currently disabled) +* ``pytest-minmax-rows``: Check that various database tables have the expected number of + records in them, and report back the actual number of records found. Requires an + existing PUDL DB. + +Running Other Commands with Make +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +There are a number of non-test ```make`` targets. To see them all open up the +``Makefile``. + +* ``ferc``: Delete all existing XBRL and DBF derived FERC databases and metadata and + re-extract them from scratch +* ``pudl``: Delete your existing ``pudl.sqlite`` and re-run the full ETL from scratch. + Assumes that the FERC DBs already exist. +* ``nuke``: delete your existing FERC and PUDL databases, rebuild + them from scratch, and run all of the tests and and data validations (akin to running + the nightly builds) for an extensive check of everything. This will take 3 hours or + more to complete, and likely fully utilize your computer's CPU and memory. +* ``install-pudl``: Remove your existing ``pudl-dev`` ``conda`` environment and + reinstall all dependencies as well as the ``catalystcoop.pudl`` package defined by + the repository in ``--editable`` mode for development. +* ``docs-build``: Remove existing PUDL documentation outputs and rebuild from scratch. +* ``dagster``: start up the Dagster UI (will remain running in your terminal until you + kill it with ``Control-C``). +* ``jlab``: start up a JupyerLab notebook server (will remain running in your terminal + until you kill it with ``Control-C``). ------------------------------------------------------------------------------- Selecting Input Data for Integration Tests @@ -194,26 +98,18 @@ default they will look in your local PUDL datastore to find it. If the data they need isn't available locally, they will download it from Zenodo and put it in the local datastore. -However, if you're editing code that affects how the datastore works, you -probably don't want to risk contaminating your working datastore. You can -use a disposable temporary datastore instead by having Tox pass the -``--tmp-data`` flag in to ``pytest`` like this: +However, if you're editing code that affects how the datastore works, you probably don't +want to risk contaminating your working datastore. You can use a disposable temporary +datastore instead by using our custom ``--tmp-data`` with ``pytest``: .. code-block:: console - $ tox -e integration -- --tmp-data - -The floating ``--`` isn't a typo, it tells Tox that you're done giving it -command line arguments, and that any additional arguments it gets should be -passed through to ``pytest``. We've configured ``pytest`` (through the -``test/conftest.py`` configuration file) to be on the lookout for the -``--tmp-data`` flag and act accordingly. + $ pytest --tmp-data test/integration .. seealso:: - * :doc:`dev_setup` for more on how to set up a PUDL workspace, including a - datastore. - * :doc:`datastore` for more on how to work with the datastore. + * :doc:`dev_setup` for more on how to set up a PUDL workspace and datastore. + * :doc:`datastore` for more on how to work with the datastore in general. ------------------------------------------------------------------------------- Data Validation @@ -231,12 +127,12 @@ an hour, depending on your computer. These tests require a fully populated PUDL database which contains all available FERC and EIA data, as specified by the ``src/pudl/package_data/settings/etl_full.yml`` input file. They are run against the "live" SQLite database in your pudl workspace at -``sqlite/pudl.sqlite``. To run the full data validation against an existing +``$PUDL_OUTPUT/pudl.sqlite``. To run the full data validation against an existing database: .. code-block:: console - $ tox -e validate + $ make pytest-validate The data validation cases that pertain to the contents of the data tables are currently stored as part of the :mod:`pudl.validate` module. @@ -249,7 +145,7 @@ Data Validation Notebooks We have a collection of Jupyter Notebooks that run the same functions as the data validation. The notebooks also produce some visualizations of the data to make it easier to understand what's wrong when validation fails. These -notebooks are stored in ``test/notebooks`` +notebooks are stored in ``test/validate/notebooks`` Like the data validations, the notebooks will only run successfully when there's a full PUDL SQLite database available in your PUDL workspace. @@ -257,18 +153,15 @@ there's a full PUDL SQLite database available in your PUDL workspace. ------------------------------------------------------------------------------- Running pytest Directly ------------------------------------------------------------------------------- -Running tests directly with ``pytest`` gives you the ability to run only -tests from a particular test module or even a single individual test case. -It's also faster because there's no testing environment to set up. Instead, -it just uses your Python environment which should be the ``pudl-dev`` conda -environment discussed in :doc:`/dev/dev_setup`. This is convenient if you're -debugging something specific or developing new test cases, but it's not as -robust as using Tox. +Running tests directly with ``pytest`` gives you the ability to run only tests from a +particular test module or even a single individual test case. It's also faster because +there's no testing environment to set up. Instead, it just uses your Python environment +which should be the ``pudl-dev`` conda environment discussed in :doc:`/dev/dev_setup`. +This is convenient if you're debugging something specific or developing new test cases. Running specific tests ^^^^^^^^^^^^^^^^^^^^^^ -To run the software unit tests with ``pytest`` directly (the same set of tests -that would be run by ``tox -e unit``): +To run the software unit tests with ``pytest`` directly: .. code-block:: console @@ -288,12 +181,11 @@ To run only the unit tests defined by a single test class within that module: Custom PUDL pytest flags ^^^^^^^^^^^^^^^^^^^^^^^^ -We have defined several custom flags to control pytest's behavior when running -the PUDL tests. They are mostly intended for use internally to specify the -behavior we want in the high level Tox test environments. +We have defined several custom flags to control pytest's behavior when running the PUDL +tests. -You can always check to see what custom flags exist by running -``pytest --help`` and looking at the ``custom options`` section: +You can always check to see what custom flags exist by running ``pytest --help`` and +looking at the ``custom options`` section: .. code-block:: console @@ -305,16 +197,15 @@ You can always check to see what custom flags exist by running --gcs-cache-path=GCS_CACHE_PATH If set, use this GCS path as a datastore cache layer. -The main flexibility that these custom options provide is in selecting where -the raw input data comes from and what data the tests should be run -against. Being able to specify the tests to run and the data to run them -against independently simplifies the test suite and keeps the data and tests -very clearly separated. +The main flexibility that these custom options provide is in selecting where the raw +input data comes from and what data the tests should be run against. Being able to +specify the tests to run and the data to run them against independently simplifies the +test suite and keeps the data and tests very clearly separated. -The ``--live-dbs`` option lets you use your existing FERC 1 and PUDL databases -instead of building a new database at all. This can be useful if you want to -test code that only operates on an existing database, and has nothing to do -with the construction of that database. For example, the output routines: +The ``--live-dbs`` option lets you use your existing FERC 1 and PUDL databases instead +of building a new database at all. This can be useful if you want to test code that only +operates on an existing database, and has nothing to do with the construction of that +database. For example, the output routines: .. code-block:: console diff --git a/environments/conda-linux-64.lock.yml b/environments/conda-linux-64.lock.yml index c6e0b59d31..9e6ab1fc9f 100644 --- a/environments/conda-linux-64.lock.yml +++ b/environments/conda-linux-64.lock.yml @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 62c018f04dcda6922fd5078faad77556aec1dd1f03c6a2262f899eff6feb9116 +# input_hash: 62bcd0fc7d50df96982d048631ad45bff7910db618111621e212e7f3c28a44bc channels: - conda-forge @@ -24,7 +24,7 @@ dependencies: - _openmp_mutex=4.5=2_gnu - fonts-conda-ecosystem=1=0 - libgcc-ng=13.2.0=h807b86a_3 - - aws-c-common=0.9.3=hd590300_0 + - aws-c-common=0.9.8=hd590300_0 - bzip2=1.0.8=hd590300_5 - c-ares=1.21.0=hd590300_0 - fribidi=1.0.10=h36c2ea0_0 @@ -67,7 +67,6 @@ dependencies: - pixman=0.42.2=h59595ed_0 - pthread-stubs=0.4=h36c2ea0_1001 - rdma-core=28.9=h59595ed_1 - - re2=2023.03.02=h8c504da_0 - snappy=1.1.10=h9fff704_0 - tzcode=2023c=h0b41bf4_0 - uriparser=0.9.7=hcb278e6_1 @@ -80,10 +79,10 @@ dependencies: - xorg-xproto=7.0.31=h7f98852_1007 - xz=5.2.6=h166bdaf_0 - yaml=0.2.5=h7f98852_2 - - aws-c-cal=0.6.2=h09139f6_2 - - aws-c-compression=0.2.17=h184a658_3 - - aws-c-sdkutils=0.1.12=h184a658_2 - - aws-checksums=0.1.17=h184a658_2 + - aws-c-cal=0.6.9=h3b91eb8_1 + - aws-c-compression=0.2.17=hfd9eb17_6 + - aws-c-sdkutils=0.1.12=hfd9eb17_5 + - aws-checksums=0.1.17=hfd9eb17_5 - expat=2.5.0=hcb278e6_1 - glog=0.6.0=h6f12383_0 - hdf4=4.2.15=h2a13503_7 @@ -96,7 +95,8 @@ dependencies: - libllvm14=14.0.6=hcd5def8_4 - libnghttp2=1.58.0=h47da74e_0 - libpng=1.6.39=h753d276_0 - - libprotobuf=4.23.4=hf27288f_6 + - libprotobuf=4.24.4=hf27288f_0 + - libre2-11=2023.06.02=h7a70373_0 - librttopo=1.1.0=hb58d41b_14 - libsqlite=3.44.0=h2797004_0 - libssh2=1.11.0=h0841786_0 @@ -105,21 +105,21 @@ dependencies: - libzip=1.10.1=h2629f0a_3 - pcre2=10.40=hc3806b6_0 - readline=8.2=h8228510_1 - - s2n=1.3.54=h06160fa_0 + - s2n=1.3.56=h06160fa_0 - tk=8.6.13=noxft_h4845f30_101 - ucx=1.15.0=h64cca9d_0 - xorg-libsm=1.2.4=h7391055_0 - zeromq=4.3.5=h59595ed_0 - zlib=1.2.13=hd590300_5 - zstd=1.5.5=hfc55251_0 - - aws-c-io=0.13.33=h161b759_0 + - aws-c-io=0.13.35=hc23c90e_8 - blosc=1.21.5=h0f2a231_0 - brotli-bin=1.1.0=hd590300_1 - freetype=2.12.1=h267a509_2 - krb5=1.21.2=h659d440_0 - libarchive=3.7.2=h039dbb9_0 - libglib=2.78.1=hebfc3b9_0 - - libgrpc=1.57.0=ha4d0f93_2 + - libllvm15=15.0.7=h5cf9203_3 - libopenblas=0.3.24=pthreads_h413a1c8_0 - libthrift=0.19.0=hb90f79a_1 - libtiff=4.6.0=ha9c0a0a_2 @@ -127,9 +127,10 @@ dependencies: - minizip=4.0.2=h0ab5242_0 - nodejs=20.8.1=h1990674_0 - nss=3.94=h1d7d5a4_0 - - orc=1.9.0=h52d3b3c_2 + - orc=1.9.0=h4b38347_4 - pandoc=3.1.3=h32600fe_0 - python=3.11.6=hab00c5b_0_cpython + - re2=2023.06.02=h2873b5e_0 - sqlite=3.44.0=h2c6b66d_0 - xorg-libx11=1.8.7=h8ee46fc_0 - aiofiles=23.2.1=pyhd8ed1ab_0 @@ -139,8 +140,8 @@ dependencies: - astroid=3.0.1=py311h38be061_0 - atk-1.0=2.38.0=hd4edc92_1 - attrs=23.1.0=pyh71513ae_1 - - aws-c-event-stream=0.3.2=h6fea174_2 - - aws-c-http=0.7.13=hb59894b_2 + - aws-c-event-stream=0.3.2=hae413d4_6 + - aws-c-http=0.7.14=h162056d_1 - backoff=2.2.1=pyhd8ed1ab_0 - backports=1.0=pyhd8ed1ab_3 - backports.zoneinfo=0.2.1=py311h38be061_8 @@ -183,7 +184,6 @@ dependencies: - gdk-pixbuf=2.42.10=h829c605_4 - google-cloud-sdk=454.0.0=py311h38be061_0 - greenlet=3.0.1=py311hb755f60_0 - - grpcio=1.57.0=py311ha6695c7_2 - gts=0.7.6=h977cf35_4 - hpack=4.0.0=pyh9f0ad1d_0 - httptools=0.6.1=py311h459d7ec_0 @@ -205,6 +205,7 @@ dependencies: - lcms2=2.15=hb7c19ff_3 - libblas=3.9.0=19_linux64_openblas - libcurl=8.4.0=hca28451_0 + - libgrpc=1.59.2=hd6c4280_0 - libpq=16.1=hfc447b1_0 - libwebp=1.3.2=h658648e_1 - llvmlite=0.41.1=py311ha6695c7_0 @@ -314,8 +315,8 @@ dependencies: - asgiref=3.7.2=pyhd8ed1ab_0 - asttokens=2.4.1=pyhd8ed1ab_0 - async-lru=2.0.4=pyhd8ed1ab_0 - - aws-c-auth=0.7.4=h1083cbe_2 - - aws-c-mqtt=0.9.7=h55cd26b_0 + - aws-c-auth=0.7.6=h37ad1db_0 + - aws-c-mqtt=0.9.9=h1387108_0 - babel=2.13.1=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 @@ -335,6 +336,7 @@ dependencies: - fonttools=4.44.0=py311h459d7ec_0 - gitdb=4.0.11=pyhd8ed1ab_0 - graphql-core=3.2.3=pyhd8ed1ab_0 + - grpcio=1.59.2=py311ha6695c7_0 - h11=0.14.0=pyhd8ed1ab_0 - h2=4.1.0=pyhd8ed1ab_0 - hdf5=1.14.2=nompi_h4f84152_100 @@ -353,7 +355,7 @@ dependencies: - latexcodec=2.0.1=pyh9f0ad1d_0 - libcblas=3.9.0=19_linux64_openblas - libgd=2.3.3=h119a65a_9 - - libgoogle-cloud=2.12.0=h8d7e28b_2 + - libgoogle-cloud=2.12.0=h5206363_4 - liblapack=3.9.0=19_linux64_openblas - linear-tsv=1.1.0=py_1 - markdown-it-py=3.0.0=pyhd8ed1ab_0 @@ -368,7 +370,7 @@ dependencies: - pip=23.3.1=pyhd8ed1ab_0 - postgresql=16.1=h8972f4a_0 - proj=9.3.0=h1d62c97_2 - - protobuf=4.23.4=py311h46cbc50_3 + - protobuf=4.24.4=py311h46cbc50_0 - psycopg2=2.9.7=py311h03dec38_1 - pyasn1-modules=0.3.0=pyhd8ed1ab_0 - pyproject_hooks=1.0.0=pyhd8ed1ab_0 @@ -398,7 +400,7 @@ dependencies: - argon2-cffi-bindings=21.2.0=py311h459d7ec_4 - arrow=1.3.0=pyhd8ed1ab_0 - async-timeout=4.0.3=pyhd8ed1ab_0 - - aws-c-s3=0.3.17=hfb4bb88_4 + - aws-c-s3=0.3.23=h7630044_1 - botocore=1.31.84=pyhd8ed1ab_0 - branca=0.7.0=pyhd8ed1ab_1 - croniter=2.0.1=pyhd8ed1ab_0 @@ -410,7 +412,7 @@ dependencies: - googleapis-common-protos=1.61.0=pyhd8ed1ab_0 - gql=3.4.1=pyhd8ed1ab_0 - graphql-relay=3.2.0=pyhd8ed1ab_0 - - grpcio-health-checking=1.57.0=pyhd8ed1ab_0 + - grpcio-health-checking=1.59.2=pyhd8ed1ab_0 - harfbuzz=8.2.1=h3d44ed6_0 - httpcore=1.0.2=pyhd8ed1ab_0 - importlib_metadata=6.8.0=hd8ed1ab_0 @@ -447,7 +449,7 @@ dependencies: - alembic=1.12.1=pyhd8ed1ab_0 - arelle-release=2.17.2=pyhd8ed1ab_0 - argon2-cffi=23.1.0=pyhd8ed1ab_0 - - aws-crt-cpp=0.24.2=ha28989d_2 + - aws-crt-cpp=0.24.5=h270613d_5 - black=23.10.1=py311h38be061_0 - bottleneck=1.3.7=py311h1f0f07a_1 - cachecontrol=0.13.1=pyhd8ed1ab_0 @@ -458,7 +460,7 @@ dependencies: - folium=0.15.0=pyhd8ed1ab_0 - google-resumable-media=2.6.0=pyhd8ed1ab_0 - graphene=3.3=pyhd8ed1ab_0 - - grpcio-status=1.57.0=pyhd8ed1ab_0 + - grpcio-status=1.59.2=pyhd8ed1ab_0 - h3-py=3.7.6=py311hb755f60_1 - httpx=0.25.1=pyhd8ed1ab_0 - identify=2.5.31=pyhd8ed1ab_0 @@ -486,7 +488,7 @@ dependencies: - typer=0.9.0=pyhd8ed1ab_0 - uvicorn-standard=0.24.0=h38be061_0 - virtualenv=20.24.6=pyhd8ed1ab_0 - - aws-sdk-cpp=1.11.156=h314d761_4 + - aws-sdk-cpp=1.11.182=h8df25a1_5 - boto3=1.28.84=pyhd8ed1ab_0 - cachecontrol-with-filecache=0.13.1=pyhd8ed1ab_0 - dagster=1.5.7=pyhd8ed1ab_0 @@ -521,7 +523,7 @@ dependencies: - graphviz=8.1.0=h28d9a01_0 - ipython=8.17.2=pyh41d4057_0 - jupyter_events=0.9.0=pyhd8ed1ab_0 - - libarrow=13.0.0=h0f80be4_7_cpu + - libarrow=14.0.1=h0406937_1_cpu - mapclassify=2.6.1=pyhd8ed1ab_0 - nbclient=0.8.0=pyhd8ed1ab_0 - recordlinkage=0.16=pyhd8ed1ab_0 @@ -531,23 +533,30 @@ dependencies: - google-cloud-core=2.3.3=pyhd8ed1ab_0 - ipykernel=6.26.0=pyhf8b6a83_0 - ipywidgets=8.1.1=pyhd8ed1ab_0 + - libarrow-acero=14.0.1=h59595ed_1_cpu + - libarrow-flight=14.0.1=h120cb0d_1_cpu + - libarrow-gandiva=14.0.1=hacb8726_1_cpu + - libparquet=14.0.1=h352af49_1_cpu - nbconvert-core=7.11.0=pyhd8ed1ab_0 - - pyarrow=13.0.0=py311h39c9aba_7_cpu - pygraphviz=1.11=py311h72a77b7_1 - tableschema=1.19.3=pyh9f0ad1d_0 - datapackage=1.15.2=pyh44b312d_0 - google-cloud-storage=2.13.0=pyhca7485f_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.10.0=pyhd8ed1ab_0 + - libarrow-dataset=14.0.1=h59595ed_1_cpu + - libarrow-flight-sql=14.0.1=h61ff412_1_cpu - nbconvert-pandoc=7.11.0=pyhd8ed1ab_0 - qtconsole-base=5.5.0=pyha770c72_0 - gcsfs=2023.10.0=pyhd8ed1ab_0 - jupyter-lsp=2.2.0=pyhd8ed1ab_0 - jupyter-resource-usage=1.0.1=pyhd8ed1ab_0 - jupyterlab_server=2.25.1=pyhd8ed1ab_0 + - libarrow-substrait=14.0.1=h61ff412_1_cpu - nbconvert=7.11.0=pyhd8ed1ab_0 - notebook-shim=0.2.3=pyhd8ed1ab_0 - jupyterlab=4.0.8=pyhd8ed1ab_0 + - pyarrow=14.0.1=py311h39c9aba_1_cpu - notebook=7.0.6=pyhd8ed1ab_0 - jupyter=1.0.0=pyhd8ed1ab_10 - sphinx-autoapi=3.0.0=pyhd8ed1ab_0 diff --git a/environments/conda-lock.yml b/environments/conda-lock.yml index 149764a1db..a9a9c8138e 100644 --- a/environments/conda-lock.yml +++ b/environments/conda-lock.yml @@ -15,9 +15,9 @@ version: 1 metadata: content_hash: - 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name: bzip2 @@ -770,19 +770,6 @@ package: sha256: 832f9393ab3144ce6468c6f150db9d398fad4451e96a8879afb3059f0c9902f6 category: main optional: false - - name: re2 - version: 2023.03.02 - manager: conda - platform: linux-64 - dependencies: - libgcc-ng: ">=12" - libstdcxx-ng: ">=12" - url: https://conda.anaconda.org/conda-forge/linux-64/re2-2023.03.02-h8c504da_0.conda - hash: - md5: 206f8fa808748f6e90599c3368a1114e - sha256: 1727f893a352ca735fb96b09f9edf6fe18c409d65550fd37e8a192919e8c827b - category: main - optional: false - name: snappy version: 1.1.10 manager: conda @@ -931,17 +918,17 @@ package: category: main optional: false - name: aws-c-cal - version: 0.6.2 + version: 0.6.9 manager: conda platform: linux-64 dependencies: - aws-c-common: ">=0.9.3,<0.9.4.0a0" + aws-c-common: ">=0.9.8,<0.9.9.0a0" libgcc-ng: ">=12" - openssl: ">=3.1.3,<4.0a0" - url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.2-h09139f6_2.conda + openssl: ">=3.1.4,<4.0a0" + url: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.9-h3b91eb8_1.conda hash: - 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name: gtk2 @@ -22396,12 +22729,13 @@ package: category: main optional: false - name: libarrow - version: 13.0.0 + version: 14.0.1 manager: conda platform: osx-arm64 dependencies: - aws-crt-cpp: ">=0.24.2,<0.24.3.0a0" - aws-sdk-cpp: ">=1.11.156,<1.11.157.0a0" + __osx: ">=10.9" + aws-crt-cpp: ">=0.24.5,<0.24.6.0a0" + aws-sdk-cpp: ">=1.11.182,<1.11.183.0a0" bzip2: ">=1.0.8,<2.0a0" glog: ">=0.6.0,<0.7.0a0" libabseil: ">=20230802.1,<20230803.0a0" @@ -22409,21 +22743,18 @@ package: libbrotlienc: ">=1.1.0,<1.2.0a0" libcxx: ">=15.0.7" libgoogle-cloud: ">=2.12.0,<2.13.0a0" - libgrpc: ">=1.57.0,<1.58.0a0" - libprotobuf: ">=4.23.4,<4.23.5.0a0" - libthrift: ">=0.19.0,<0.19.1.0a0" + libre2-11: ">=2023.6.2,<2024.0a0" libutf8proc: ">=2.8.0,<3.0a0" libzlib: ">=1.2.13,<1.3.0a0" lz4-c: ">=1.9.3,<1.10.0a0" - openssl: ">=3.1.3,<4.0a0" orc: ">=1.9.0,<1.9.1.0a0" - re2: ">=2023.3.2,<2023.3.3.0a0" + re2: "" snappy: ">=1.1.10,<2.0a0" zstd: ">=1.5.5,<1.6.0a0" - url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-13.0.0-hf4fadc0_7_cpu.conda + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-14.0.1-h7bb5718_1_cpu.conda hash: - md5: 4159ab8fc4fa8f483f01bd3a75d7bf0f - sha256: 1ce9cf1d41f380bae6cdccdb0f61f6286b453320a8c32237b030b810ded55a4b + md5: 11122c7985ba7511d63df5f2cad917fa + sha256: b07036659cb3492f753c93fdd0da6b8ae177e1ec55cb1208b5d02d63bf80723d category: main optional: false - name: matplotlib-base @@ -22758,6 +23089,72 @@ package: sha256: 713f0cc927a862862a6d35bfb29c4114f987e4f59e2a8a14f71f23fcd7edfec3 category: main optional: false + - name: libarrow-acero + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libcxx: ">=15.0.7" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-acero-14.0.1-had9dd58_1_cpu.conda + hash: + md5: dab478b07c494888aa403fb439a5dada + sha256: c1be980876224a1de110688ae1288de10cce5a982c110341e982e6e1654ff596 + category: main + optional: false + - name: libarrow-flight + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libabseil: ">=20230802.1,<20230803.0a0" + libarrow: 14.0.1 + libcxx: ">=15.0.7" + libgrpc: ">=1.59.2,<1.60.0a0" + libprotobuf: ">=4.24.4,<4.24.5.0a0" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-flight-14.0.1-h1011bfc_1_cpu.conda + hash: + md5: 795d8f2bb1049ab37dab1e2656df6a23 + sha256: fff9bd3f6c91f44aaa84cd4319c3ef1dd730e08108416fac7be8f70601fe176c + category: main + optional: false + - name: libarrow-gandiva + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libcxx: ">=15.0.7" + libllvm15: ">=15.0.7,<15.1.0a0" + libre2-11: ">=2023.6.2,<2024.0a0" + libutf8proc: ">=2.8.0,<3.0a0" + openssl: ">=3.1.4,<4.0a0" + re2: "" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-gandiva-14.0.1-h2b96968_1_cpu.conda + hash: + md5: 7b44f16df2e1955867a7930a9bda72c5 + sha256: f73bd5e13ff048cdc8ad5506a3fa3e8f079bb5276db080edb225c1de74abb094 + category: main + optional: false + - name: libparquet + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libcxx: ">=15.0.7" + libthrift: ">=0.19.0,<0.19.1.0a0" + openssl: ">=3.1.4,<4.0a0" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libparquet-14.0.1-heaab74a_1_cpu.conda + hash: + md5: 29ec8382d4d8da63ded09a173c635087 + sha256: a9cbe2f62f01fd6ab974f3ba65995e8d64bf53b65c9fad26f9e1ad403dce0ea8 + category: main + optional: false - name: mapclassify version: 2.6.1 manager: conda @@ -22791,22 +23188,6 @@ package: sha256: 4ebd237cdf4bfa5226f92d2ae78fab8dba27696909391884dc6594ca6f9df5ff category: main optional: false - - name: pyarrow - version: 13.0.0 - manager: conda - platform: osx-arm64 - dependencies: - libarrow: 13.0.0 - libcxx: ">=15.0.7" - numpy: ">=1.23.5,<2.0a0" - python: ">=3.11,<3.12.0a0" - python_abi: 3.11.* - url: https://conda.anaconda.org/conda-forge/osx-arm64/pyarrow-13.0.0-py311hd7bc329_7_cpu.conda - hash: - md5: 4dcaa7f7be49ada17a2196e59bbc2de0 - sha256: cddca7e20ca4a94eab958780f22dd5e4b24ae10322b928c138b5a09d05ff6f56 - category: main - optional: false - name: pygraphviz version: "1.11" manager: conda @@ -22958,6 +23339,38 @@ package: sha256: 8136defec115396ba992273a77f814d74eeafd9cc099f5430d109c60785a7f02 category: main optional: false + - name: libarrow-dataset + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libarrow-acero: 14.0.1 + libcxx: ">=15.0.7" + libparquet: 14.0.1 + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-dataset-14.0.1-had9dd58_1_cpu.conda + hash: + md5: 710b15572b65ca7f7fae5e53ea10576a + sha256: 90230a77d8c7752ede5a3742d7e58af4da490dd0adfd6d1108b1d2b8e7f51147 + category: main + optional: false + - name: libarrow-flight-sql + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libarrow-flight: 14.0.1 + libcxx: ">=15.0.7" + libprotobuf: ">=4.24.4,<4.24.5.0a0" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-flight-sql-14.0.1-h660fe36_1_cpu.conda + hash: + md5: 369f206a2b446232c90963a9545d3cbc + sha256: 03a96a17e0202be09864c15b4e9729c27ca15b192ad021bbdf4c5b1355fea51a + category: main + optional: false - name: nbconvert-core version: 7.11.0 manager: conda @@ -23098,6 +23511,23 @@ package: sha256: 0b9a72f28ff8a12e6ea0ae43d3ea93e288074d29348c5fc6fbb3a5e5e18b2ecd category: main optional: false + - name: libarrow-substrait + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libarrow-acero: 14.0.1 + libarrow-dataset: 14.0.1 + libcxx: ">=15.0.7" + libprotobuf: ">=4.24.4,<4.24.5.0a0" + url: https://conda.anaconda.org/conda-forge/osx-arm64/libarrow-substrait-14.0.1-h594d712_1_cpu.conda + hash: + md5: c727e569e0812a90c7321ae79e387843 + sha256: 49c6e1477c59334222fd25730b942e0dfb4b5bfba79fc173bc5ab5ba09e7a671 + category: main + optional: false - name: nbconvert-pandoc version: 7.11.0 manager: conda @@ -23226,6 +23656,30 @@ package: sha256: f028d7ad1f2175cde307db08b60d07e371b9d6f035cfae6c81ea94b4c408c538 category: main optional: false + - name: pyarrow + version: 14.0.1 + manager: conda + platform: osx-arm64 + dependencies: + __osx: ">=10.9" + libarrow: 14.0.1 + libarrow-acero: 14.0.1 + libarrow-dataset: 14.0.1 + libarrow-flight: 14.0.1 + libarrow-flight-sql: 14.0.1 + libarrow-gandiva: 14.0.1 + libarrow-substrait: 14.0.1 + libcxx: ">=15.0.7" + libparquet: 14.0.1 + numpy: ">=1.23.5,<2.0a0" + python: ">=3.11,<3.12.0a0" + python_abi: 3.11.* + url: https://conda.anaconda.org/conda-forge/osx-arm64/pyarrow-14.0.1-py311h637fcfe_1_cpu.conda + hash: + md5: 2e1207c4a320d41c7676e46f33306483 + sha256: d674b26018f29e37d3794124c79981c295642b389b9c3a55073cdeae71d0d606 + category: main + optional: false - name: jupyterlab version: 4.0.8 manager: conda diff --git a/environments/conda-osx-64.lock.yml b/environments/conda-osx-64.lock.yml index c3a4514e48..1e7c353eac 100644 --- a/environments/conda-osx-64.lock.yml +++ b/environments/conda-osx-64.lock.yml @@ -1,12 +1,12 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: 7ade47c1ca071082a3818606e76b6768241ac2410e31d8f902abbb59ecaba073 +# input_hash: bcf38db86781af22df7f496ce0dafe43a905c359e9c7d6d038429569b874c305 channels: - conda-forge - defaults dependencies: - - aws-c-common=0.9.3=h0dc2134_0 + - aws-c-common=0.9.8=h10d778d_0 - bzip2=1.0.8=h10d778d_5 - c-ares=1.21.0=h10d778d_0 - ca-certificates=2023.7.22=h8857fd0_0 @@ -44,10 +44,10 @@ dependencies: - xorg-libxdmcp=1.1.3=h35c211d_0 - xz=5.2.6=h775f41a_0 - yaml=0.2.5=h0d85af4_2 - - aws-c-cal=0.6.2=hfc10710_2 - - aws-c-compression=0.2.17=hd41bdd4_3 - - aws-c-sdkutils=0.1.12=hd41bdd4_2 - - aws-checksums=0.1.17=hd41bdd4_2 + - aws-c-cal=0.6.9=h49e9720_1 + - aws-c-compression=0.2.17=hff1f2c8_6 + - aws-c-sdkutils=0.1.12=hff1f2c8_5 + - aws-checksums=0.1.17=hff1f2c8_5 - expat=2.5.0=hf0c8a7f_1 - fonts-conda-forge=1=0 - geos=3.12.0=he965462_0 @@ -75,14 +75,13 @@ dependencies: - pandoc=3.1.3=h9d075a6_0 - pcre2=10.40=h1c4e4bc_0 - pixman=0.42.2=he965462_0 - - re2=2023.03.02=h096449b_0 - snappy=1.1.10=h225ccf5_0 - tk=8.6.13=h1abcd95_1 - uriparser=0.9.7=hf0c8a7f_1 - zeromq=4.3.5=h93d8f39_0 - zlib=1.2.13=h8a1eda9_5 - zstd=1.5.5=h829000d_0 - - aws-c-io=0.13.33=h2566903_0 + - aws-c-io=0.13.35=hb98174f_8 - blosc=1.21.5=heccf04b_0 - brotli-bin=1.1.0=h0dc2134_1 - fonts-conda-ecosystem=1=0 @@ -94,8 +93,10 @@ dependencies: - libgfortran=5.0.0=13_2_0_h97931a8_1 - libglib=2.78.1=h6d9ecee_0 - libkml=1.3.0=hab3ca0e_1018 + - libllvm15=15.0.7=he4b1e75_3 - libnghttp2=1.58.0=h64cf6d3_0 - - libprotobuf=4.23.4=he0c2237_6 + - libprotobuf=4.24.4=h0ee05dc_0 + - libre2-11=2023.06.02=h4694dbf_0 - librttopo=1.1.0=h23f359d_14 - libssh2=1.11.0=hd019ec5_0 - libtiff=4.6.0=h684deea_2 @@ -106,8 +107,8 @@ dependencies: - nss=3.94=hd6ac835_0 - readline=8.2=h9e318b2_1 - atk-1.0=2.38.0=h1d18e73_1 - - aws-c-event-stream=0.3.2=he52df9d_2 - - aws-c-http=0.7.13=hb43ddd7_2 + - aws-c-event-stream=0.3.2=hb6e475e_6 + - aws-c-http=0.7.14=h950a07a_1 - brotli=1.1.0=h0dc2134_1 - fontconfig=2.14.2=h5bb23bf_0 - freexl=2.0.0=h3ec172f_0 @@ -115,14 +116,14 @@ dependencies: - gts=0.7.6=h53e17e3_4 - krb5=1.21.2=hb884880_0 - lcms2=2.15=hd6ba6f3_3 - - libgrpc=1.57.0=h7cc5909_2 - libopenblas=0.3.24=openmp_h48a4ad5_0 - libthrift=0.19.0=h064b379_1 - libwebp=1.3.2=h44782d1_1 - openjpeg=2.5.0=ha4da562_3 - - orc=1.9.0=ha4ae40d_2 + - orc=1.9.0=hd1092d7_4 - prettier=3.1.0=hbd11d21_0 - python=3.11.6=h30d4d87_0_cpython + - re2=2023.06.02=hd34609a_0 - sqlite=3.44.0=h7461747_0 - aiofiles=23.2.1=pyhd8ed1ab_0 - alabaster=0.7.13=pyhd8ed1ab_0 @@ -131,8 +132,8 @@ dependencies: - appnope=0.1.3=pyhd8ed1ab_0 - astroid=3.0.1=py311h6eed73b_0 - attrs=23.1.0=pyh71513ae_1 - - aws-c-auth=0.7.4=hbe6ead2_2 - - aws-c-mqtt=0.9.7=h6b10715_0 + - aws-c-auth=0.7.6=hc3630cc_0 + - aws-c-mqtt=0.9.9=h5e4a26e_0 - backoff=2.2.1=pyhd8ed1ab_0 - backports=1.0=pyhd8ed1ab_3 - backports.zoneinfo=0.2.1=py311h6eed73b_8 @@ -171,7 +172,6 @@ dependencies: - fsspec=2023.10.0=pyhca7485f_0 - google-cloud-sdk=454.0.0=py311h6eed73b_0 - greenlet=3.0.1=py311hd39e593_0 - - grpcio=1.57.0=py311h78ff076_2 - hpack=4.0.0=pyh9f0ad1d_0 - httptools=0.6.1=py311he705e18_0 - humanfriendly=10.0=pyhd8ed1ab_6 @@ -191,6 +191,7 @@ dependencies: - libblas=3.9.0=19_osx64_openblas - libcurl=8.4.0=h726d00d_0 - libgd=2.3.3=h0dceb68_9 + - libgrpc=1.59.2=ha7f534c_0 - libpq=16.1=h6dd4ff7_0 - llvmlite=0.41.1=py311hb5c2e0a_0 - locket=1.0.0=pyhd8ed1ab_0 @@ -295,7 +296,7 @@ dependencies: - asgiref=3.7.2=pyhd8ed1ab_0 - asttokens=2.4.1=pyhd8ed1ab_0 - async-lru=2.0.4=pyhd8ed1ab_0 - - aws-c-s3=0.3.17=h5800b94_4 + - aws-c-s3=0.3.23=hb1cbb54_1 - babel=2.13.1=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 @@ -314,6 +315,7 @@ dependencies: - fonttools=4.44.0=py311he705e18_0 - gitdb=4.0.11=pyhd8ed1ab_0 - graphql-core=3.2.3=pyhd8ed1ab_0 + - grpcio=1.59.2=py311hfd95bfa_0 - h11=0.14.0=pyhd8ed1ab_0 - h2=4.1.0=pyhd8ed1ab_0 - harfbuzz=8.2.1=h7666e2a_0 @@ -332,7 +334,7 @@ dependencies: - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 - latexcodec=2.0.1=pyh9f0ad1d_0 - libcblas=3.9.0=19_osx64_openblas - - libgoogle-cloud=2.12.0=hc7e40ee_2 + - libgoogle-cloud=2.12.0=hc0857f6_4 - liblapack=3.9.0=19_osx64_openblas - linear-tsv=1.1.0=py_1 - markdown-it-py=3.0.0=pyhd8ed1ab_0 @@ -347,7 +349,7 @@ dependencies: - poppler=23.10.0=hdd5a5e8_0 - postgresql=16.1=h413614c_0 - proj=9.3.0=h23b96cc_2 - - protobuf=4.23.4=py311h01dfb71_3 + - protobuf=4.24.4=py311h021eaf5_0 - psycopg2=2.9.7=py311h187f0af_1 - pyasn1-modules=0.3.0=pyhd8ed1ab_0 - pyobjc-core=10.0=py311hf110eff_0 @@ -378,7 +380,7 @@ dependencies: - argon2-cffi-bindings=21.2.0=py311h2725bcf_4 - arrow=1.3.0=pyhd8ed1ab_0 - async-timeout=4.0.3=pyhd8ed1ab_0 - - aws-crt-cpp=0.24.2=hf47b73b_2 + - aws-crt-cpp=0.24.5=h7eda119_5 - botocore=1.31.84=pyhd8ed1ab_0 - branca=0.7.0=pyhd8ed1ab_1 - croniter=2.0.1=pyhd8ed1ab_0 @@ -390,7 +392,7 @@ dependencies: - googleapis-common-protos=1.61.0=pyhd8ed1ab_0 - gql=3.4.1=pyhd8ed1ab_0 - graphql-relay=3.2.0=pyhd8ed1ab_0 - - grpcio-health-checking=1.57.0=pyhd8ed1ab_0 + - grpcio-health-checking=1.59.2=pyhd8ed1ab_0 - httpcore=1.0.2=pyhd8ed1ab_0 - importlib_metadata=6.8.0=hd8ed1ab_0 - jsonschema-specifications=2023.7.1=pyhd8ed1ab_0 @@ -427,7 +429,7 @@ dependencies: - alembic=1.12.1=pyhd8ed1ab_0 - arelle-release=2.17.2=pyhd8ed1ab_0 - argon2-cffi=23.1.0=pyhd8ed1ab_0 - - aws-sdk-cpp=1.11.156=hf61f2bb_4 + - aws-sdk-cpp=1.11.182=h8f92232_5 - black=23.10.1=py311h6eed73b_0 - bottleneck=1.3.7=py311h4a70a88_1 - cachecontrol=0.13.1=pyhd8ed1ab_0 @@ -438,7 +440,7 @@ dependencies: - folium=0.15.0=pyhd8ed1ab_0 - google-resumable-media=2.6.0=pyhd8ed1ab_0 - graphene=3.3=pyhd8ed1ab_0 - - grpcio-status=1.57.0=pyhd8ed1ab_0 + - grpcio-status=1.59.2=pyhd8ed1ab_0 - gtk2=2.24.33=h7c1209e_2 - h3-py=3.7.6=py311hdf8f085_1 - httpx=0.25.1=pyhd8ed1ab_0 @@ -482,7 +484,7 @@ dependencies: - graphviz=8.1.0=hc7f41f9_0 - jsonschema-with-format-nongpl=4.19.2=pyhd8ed1ab_0 - jupyter_client=8.6.0=pyhd8ed1ab_0 - - libarrow=13.0.0=h66f826e_7_cpu + - libarrow=14.0.1=hcf474e5_1_cpu - matplotlib-base=3.8.1=py311hd316c10_0 - nbformat=5.9.2=pyhd8ed1ab_0 - pandera-core=0.17.2=pyhd8ed1ab_1 @@ -500,9 +502,12 @@ dependencies: - google-auth-oauthlib=1.1.0=pyhd8ed1ab_0 - ipython=8.17.2=pyh31c8845_0 - jupyter_events=0.9.0=pyhd8ed1ab_0 + - libarrow-acero=14.0.1=hc222712_1_cpu + - libarrow-flight=14.0.1=ha1803ca_1_cpu + - libarrow-gandiva=14.0.1=heeebe7c_1_cpu + - libparquet=14.0.1=h27bd29f_1_cpu - mapclassify=2.6.1=pyhd8ed1ab_0 - nbclient=0.8.0=pyhd8ed1ab_0 - - pyarrow=13.0.0=py311h54e7ce8_7_cpu - pygraphviz=1.11=py311hc6eba27_1 - recordlinkage=0.16=pyhd8ed1ab_0 - tabulator=1.53.5=pyhd8ed1ab_0 @@ -511,12 +516,15 @@ dependencies: - google-cloud-core=2.3.3=pyhd8ed1ab_0 - ipykernel=6.26.0=pyh3cd1d5f_0 - ipywidgets=8.1.1=pyhd8ed1ab_0 + - libarrow-dataset=14.0.1=hc222712_1_cpu + - libarrow-flight-sql=14.0.1=h8ec153b_1_cpu - nbconvert-core=7.11.0=pyhd8ed1ab_0 - tableschema=1.19.3=pyh9f0ad1d_0 - datapackage=1.15.2=pyh44b312d_0 - google-cloud-storage=2.13.0=pyhca7485f_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.10.0=pyhd8ed1ab_0 + - libarrow-substrait=14.0.1=h8ec153b_1_cpu - nbconvert-pandoc=7.11.0=pyhd8ed1ab_0 - qtconsole-base=5.5.0=pyha770c72_0 - gcsfs=2023.10.0=pyhd8ed1ab_0 @@ -525,6 +533,7 @@ dependencies: - jupyterlab_server=2.25.1=pyhd8ed1ab_0 - nbconvert=7.11.0=pyhd8ed1ab_0 - notebook-shim=0.2.3=pyhd8ed1ab_0 + - pyarrow=14.0.1=py311h98a0319_1_cpu - jupyterlab=4.0.8=pyhd8ed1ab_0 - notebook=7.0.6=pyhd8ed1ab_0 - jupyter=1.0.0=pyhd8ed1ab_10 diff --git a/environments/conda-osx-arm64.lock.yml b/environments/conda-osx-arm64.lock.yml index 0575e8a568..a9537c10fb 100644 --- a/environments/conda-osx-arm64.lock.yml +++ b/environments/conda-osx-arm64.lock.yml @@ -1,12 +1,12 @@ # Generated by conda-lock. # platform: osx-arm64 -# input_hash: 1678be4da0075835c5823bcfd307ec83872e5ae2ab716ed9f2b6d9f176a89e0d +# input_hash: 8d8eb4c72944efa02bab31f0274acad445146594b4cad129cc341a304e08ebb2 channels: - conda-forge - defaults dependencies: - - aws-c-common=0.9.3=hb547adb_0 + - aws-c-common=0.9.8=h93a5062_0 - bzip2=1.0.8=h93a5062_5 - c-ares=1.21.0=h93a5062_0 - ca-certificates=2023.7.22=hf0a4a13_0 @@ -45,10 +45,10 @@ dependencies: - xorg-libxdmcp=1.1.3=h27ca646_0 - xz=5.2.6=h57fd34a_0 - yaml=0.2.5=h3422bc3_2 - - aws-c-cal=0.6.2=h12c43c8_2 - - aws-c-compression=0.2.17=h12c43c8_3 - - aws-c-sdkutils=0.1.12=h12c43c8_2 - - aws-checksums=0.1.17=h12c43c8_2 + - aws-c-cal=0.6.9=hea61927_1 + - aws-c-compression=0.2.17=hea61927_6 + - aws-c-sdkutils=0.1.12=hea61927_5 + - aws-checksums=0.1.17=hea61927_5 - expat=2.5.0=hb7217d7_1 - fonts-conda-forge=1=0 - geos=3.12.0=h13dd4ca_0 @@ -75,14 +75,13 @@ dependencies: - openssl=3.1.4=h0d3ecfb_0 - pcre2=10.40=hb34f9b4_0 - pixman=0.42.2=h13dd4ca_0 - - re2=2023.03.02=hc5e2d97_0 - snappy=1.1.10=h17c5cce_0 - tk=8.6.13=h5083fa2_1 - uriparser=0.9.7=hb7217d7_1 - zeromq=4.3.5=h965bd2d_0 - zlib=1.2.13=h53f4e23_5 - zstd=1.5.5=h4f39d0f_0 - - aws-c-io=0.13.33=h5bd1e48_0 + - aws-c-io=0.13.35=he1b4ce3_8 - blosc=1.21.5=hc338f07_0 - brotli-bin=1.1.0=hb547adb_1 - fonts-conda-ecosystem=1=0 @@ -94,8 +93,10 @@ dependencies: - libgfortran=5.0.0=13_2_0_hd922786_1 - libglib=2.78.1=hd9b11f9_0 - libkml=1.3.0=h1eb4d9f_1018 + - libllvm15=15.0.7=h504e6bf_3 - libnghttp2=1.58.0=ha4dd798_0 - - libprotobuf=4.23.4=hf590ac1_6 + - libprotobuf=4.24.4=hc9861d8_0 + - libre2-11=2023.06.02=h1753957_0 - librttopo=1.1.0=h667cd51_14 - libssh2=1.11.0=h7a5bd25_0 - libtiff=4.6.0=ha8a6c65_2 @@ -106,8 +107,8 @@ dependencies: - nss=3.94=hc6b9969_0 - readline=8.2=h92ec313_1 - atk-1.0=2.38.0=hcb7b3dd_1 - - aws-c-event-stream=0.3.2=h8f67f9a_2 - - aws-c-http=0.7.13=h7dae168_2 + - aws-c-event-stream=0.3.2=h32206d9_6 + - aws-c-http=0.7.14=h673bc1b_1 - brotli=1.1.0=hb547adb_1 - fontconfig=2.14.2=h82840c6_0 - freexl=2.0.0=hfbad9fb_0 @@ -115,14 +116,14 @@ dependencies: - gts=0.7.6=he42f4ea_4 - krb5=1.21.2=h92f50d5_0 - lcms2=2.15=hf2736f0_3 - - libgrpc=1.57.0=hbf2b313_2 - libopenblas=0.3.24=openmp_hd76b1f2_0 - libthrift=0.19.0=h026a170_1 - libwebp=1.3.2=hf30222e_1 - openjpeg=2.5.0=h4c1507b_3 - - orc=1.9.0=hbfdecac_2 + - orc=1.9.0=h7c018df_4 - prettier=3.1.0=hb67532b_0 - python=3.11.6=h47c9636_0_cpython + - re2=2023.06.02=h6135d0a_0 - sqlite=3.44.0=hf2abe2d_0 - aiofiles=23.2.1=pyhd8ed1ab_0 - alabaster=0.7.13=pyhd8ed1ab_0 @@ -131,8 +132,8 @@ dependencies: - appnope=0.1.3=pyhd8ed1ab_0 - astroid=3.0.1=py311h267d04e_0 - attrs=23.1.0=pyh71513ae_1 - - aws-c-auth=0.7.4=h3e84773_2 - - aws-c-mqtt=0.9.7=h9e52e49_0 + - aws-c-auth=0.7.6=h30f9597_0 + - aws-c-mqtt=0.9.9=h2364c62_0 - backoff=2.2.1=pyhd8ed1ab_0 - backports=1.0=pyhd8ed1ab_3 - backports.zoneinfo=0.2.1=py311h267d04e_8 @@ -171,7 +172,6 @@ dependencies: - fsspec=2023.10.0=pyhca7485f_0 - google-cloud-sdk=454.0.0=py311h267d04e_0 - greenlet=3.0.1=py311hbaf5611_0 - - grpcio=1.57.0=py311h79dd126_2 - hpack=4.0.0=pyh9f0ad1d_0 - httptools=0.6.1=py311h05b510d_0 - humanfriendly=10.0=pyhd8ed1ab_6 @@ -191,6 +191,7 @@ dependencies: - libblas=3.9.0=19_osxarm64_openblas - libcurl=8.4.0=h2d989ff_0 - libgd=2.3.3=hfdf3952_9 + - libgrpc=1.59.2=hbcf6334_0 - libpq=16.1=hd435d45_0 - llvmlite=0.41.1=py311hf5d242d_0 - locket=1.0.0=pyhd8ed1ab_0 @@ -295,7 +296,7 @@ dependencies: - asgiref=3.7.2=pyhd8ed1ab_0 - asttokens=2.4.1=pyhd8ed1ab_0 - async-lru=2.0.4=pyhd8ed1ab_0 - - aws-c-s3=0.3.17=h29c26b6_4 + - aws-c-s3=0.3.23=h3940a1a_1 - babel=2.13.1=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 @@ -314,6 +315,7 @@ dependencies: - fonttools=4.44.0=py311h05b510d_0 - gitdb=4.0.11=pyhd8ed1ab_0 - graphql-core=3.2.3=pyhd8ed1ab_0 + - grpcio=1.59.2=py311h79dd126_0 - h11=0.14.0=pyhd8ed1ab_0 - h2=4.1.0=pyhd8ed1ab_0 - harfbuzz=8.2.1=hf1a6348_0 @@ -332,7 +334,7 @@ dependencies: - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 - latexcodec=2.0.1=pyh9f0ad1d_0 - libcblas=3.9.0=19_osxarm64_openblas - - libgoogle-cloud=2.12.0=hde42cda_2 + - libgoogle-cloud=2.12.0=hfb399a7_4 - liblapack=3.9.0=19_osxarm64_openblas - linear-tsv=1.1.0=py_1 - markdown-it-py=3.0.0=pyhd8ed1ab_0 @@ -347,7 +349,7 @@ dependencies: - poppler=23.10.0=hcdd998b_0 - postgresql=16.1=hc6ab77f_0 - proj=9.3.0=h52fb9d0_2 - - protobuf=4.23.4=py311h590876e_3 + - protobuf=4.24.4=py311h4d1eceb_0 - psycopg2=2.9.7=py311h589e011_1 - pyasn1-modules=0.3.0=pyhd8ed1ab_0 - pyobjc-core=10.0=py311hb702dc4_0 @@ -378,7 +380,7 @@ dependencies: - argon2-cffi-bindings=21.2.0=py311heffc1b2_4 - arrow=1.3.0=pyhd8ed1ab_0 - async-timeout=4.0.3=pyhd8ed1ab_0 - - aws-crt-cpp=0.24.2=hbe5f050_2 + - aws-crt-cpp=0.24.5=h8bfa36e_5 - botocore=1.31.84=pyhd8ed1ab_0 - branca=0.7.0=pyhd8ed1ab_1 - croniter=2.0.1=pyhd8ed1ab_0 @@ -390,7 +392,7 @@ dependencies: - googleapis-common-protos=1.61.0=pyhd8ed1ab_0 - gql=3.4.1=pyhd8ed1ab_0 - graphql-relay=3.2.0=pyhd8ed1ab_0 - - grpcio-health-checking=1.57.0=pyhd8ed1ab_0 + - grpcio-health-checking=1.59.2=pyhd8ed1ab_0 - httpcore=1.0.2=pyhd8ed1ab_0 - importlib_metadata=6.8.0=hd8ed1ab_0 - jsonschema-specifications=2023.7.1=pyhd8ed1ab_0 @@ -427,7 +429,7 @@ dependencies: - alembic=1.12.1=pyhd8ed1ab_0 - arelle-release=2.17.2=pyhd8ed1ab_0 - argon2-cffi=23.1.0=pyhd8ed1ab_0 - - aws-sdk-cpp=1.11.156=ha282cf0_4 + - aws-sdk-cpp=1.11.182=h2baef6e_5 - black=23.10.1=py311h267d04e_0 - bottleneck=1.3.7=py311hb49d859_1 - cachecontrol=0.13.1=pyhd8ed1ab_0 @@ -438,7 +440,7 @@ dependencies: - folium=0.15.0=pyhd8ed1ab_0 - google-resumable-media=2.6.0=pyhd8ed1ab_0 - graphene=3.3=pyhd8ed1ab_0 - - grpcio-status=1.57.0=pyhd8ed1ab_0 + - grpcio-status=1.59.2=pyhd8ed1ab_0 - gtk2=2.24.33=h57013de_2 - h3-py=3.7.6=py311ha891d26_1 - httpx=0.25.1=pyhd8ed1ab_0 @@ -482,7 +484,7 @@ dependencies: - graphviz=8.1.0=h10878c0_0 - jsonschema-with-format-nongpl=4.19.2=pyhd8ed1ab_0 - jupyter_client=8.6.0=pyhd8ed1ab_0 - - libarrow=13.0.0=hf4fadc0_7_cpu + - libarrow=14.0.1=h7bb5718_1_cpu - matplotlib-base=3.8.1=py311hfdba5f6_0 - nbformat=5.9.2=pyhd8ed1ab_0 - pandera-core=0.17.2=pyhd8ed1ab_1 @@ -500,9 +502,12 @@ dependencies: - google-auth-oauthlib=1.1.0=pyhd8ed1ab_0 - ipython=8.17.2=pyh31c8845_0 - jupyter_events=0.9.0=pyhd8ed1ab_0 + - libarrow-acero=14.0.1=had9dd58_1_cpu + - libarrow-flight=14.0.1=h1011bfc_1_cpu + - libarrow-gandiva=14.0.1=h2b96968_1_cpu + - libparquet=14.0.1=heaab74a_1_cpu - mapclassify=2.6.1=pyhd8ed1ab_0 - nbclient=0.8.0=pyhd8ed1ab_0 - - pyarrow=13.0.0=py311hd7bc329_7_cpu - pygraphviz=1.11=py311h5178850_1 - recordlinkage=0.16=pyhd8ed1ab_0 - tabulator=1.53.5=pyhd8ed1ab_0 @@ -511,12 +516,15 @@ dependencies: - google-cloud-core=2.3.3=pyhd8ed1ab_0 - ipykernel=6.26.0=pyh3cd1d5f_0 - ipywidgets=8.1.1=pyhd8ed1ab_0 + - libarrow-dataset=14.0.1=had9dd58_1_cpu + - libarrow-flight-sql=14.0.1=h660fe36_1_cpu - nbconvert-core=7.11.0=pyhd8ed1ab_0 - tableschema=1.19.3=pyh9f0ad1d_0 - datapackage=1.15.2=pyh44b312d_0 - google-cloud-storage=2.13.0=pyhca7485f_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.10.0=pyhd8ed1ab_0 + - libarrow-substrait=14.0.1=h594d712_1_cpu - nbconvert-pandoc=7.11.0=pyhd8ed1ab_0 - qtconsole-base=5.5.0=pyha770c72_0 - gcsfs=2023.10.0=pyhd8ed1ab_0 @@ -525,6 +533,7 @@ dependencies: - jupyterlab_server=2.25.1=pyhd8ed1ab_0 - nbconvert=7.11.0=pyhd8ed1ab_0 - notebook-shim=0.2.3=pyhd8ed1ab_0 + - pyarrow=14.0.1=py311h637fcfe_1_cpu - jupyterlab=4.0.8=pyhd8ed1ab_0 - notebook=7.0.6=pyhd8ed1ab_0 - jupyter=1.0.0=pyhd8ed1ab_10 diff --git a/pyproject.toml b/pyproject.toml index a90f78daee..9dde334c93 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,9 +33,9 @@ dependencies = [ "furo>=2022.4.7", "gcsfs>=2023", "geopandas>=0.14", - "grpcio==1.57.0", # Required by dagster, binary dependencies are flaky - "grpcio-health-checking==1.57.0", # Required by dagster, binary dependencies are flaky - "grpcio-status==1.57.0", # Required by dagster, binary dependencies are flaky + "grpcio==1.59.2", # Required by dagster, binary dependencies are flaky + "grpcio-health-checking==1.59.2", # Required by dagster, binary dependencies are flaky + "grpcio-status==1.59.2", # Required by dagster, binary dependencies are flaky "hypothesis>=6.87,<7.0", "jinja2>=3.1", "jupyter", @@ -50,7 +50,7 @@ dependencies = [ "pandas>=2.1", "pandera>=0.17.2", "pre-commit>=3", - "pyarrow>=13", # pandas[parquet] + "pyarrow>=14.0.1", # pandas[parquet] "pydantic>=1.10,<2", # Required after pandera-core is retired and we switch to pydantic v2 #"pydantic>=2.4", diff --git a/tox.ini b/tox.ini deleted file mode 100644 index b4e6a5bc61..0000000000 --- a/tox.ini +++ /dev/null @@ -1,250 +0,0 @@ -[tox] -envlist = ci - -[testenv] -allowlist_externals = - bash - coverage - sphinx-build - twine -# shared directory for re-used packages -envdir = {toxinidir}/.env_tox -passenv = - CI - CLOUDSDK_* - CONDA_PREFIX - DAGSTER_HOME - GITHUB_* - GOOGLE_* - GCLOUD_* - GCP_* - HOME - PUDL_INPUT - PUDL_OUTPUT - SQLALCHEMY_WARN_20 -covargs = --cov={envsitepackagesdir}/pudl --cov-report=xml -covreport = coverage report --sort=cover - -########################################################################### -# Code and Documentation Linters -########################################################################### -[testenv:ruff] -description = Run the ruff linter on the entire PUDL codebase -skip_install = false -extras = - test -commands = - ruff check ./ - -[testenv:pre_commit] -description = Run git pre-commit hooks not covered by the other linters. -skip_install = false -extras = - test -commands = - pre-commit run --all-files --show-diff-on-failure check-merge-conflict - pre-commit run --all-files --show-diff-on-failure check-yaml - pre-commit run --all-files --show-diff-on-failure check-case-conflict - pre-commit run --all-files --show-diff-on-failure debug-statements - pre-commit run --all-files --show-diff-on-failure name-tests-test - -[testenv:linters] -description = Run the pre-commit and ruff linters -skip_install = false -extras = - {[testenv:pre_commit]extras} - {[testenv:ruff]extras} -commands = - {[testenv:pre_commit]commands} - {[testenv:ruff]commands} - -########################################################################### -# Lint and Build the Docs -########################################################################### -[testenv:doc8] -description = Check the documentation input files for syntactical correctness. -skip_install = false -extras = - docs -commands = - doc8 docs/ README.rst - -[testenv:docs] -description = Build the PUDL HTML docs from scratch using Sphinx. -skip_install = false -extras = - test - {[testenv:doc8]extras} -commands = - coverage erase - bash -c 'rm -rf docs/_build' - {[testenv:doc8]commands} - bash -c 'coverage run --source={envsitepackagesdir}/pudl -- $(which sphinx-build) -W -b html docs docs/_build/html' - coverage xml - - -########################################################################### -# Test the code and validate data -########################################################################### -[testenv:unit] -description = Run all the software unit tests. -extras = - test -commands = - pytest {tty:--color=yes} {posargs} {[testenv]covargs} \ - --doctest-modules {envsitepackagesdir}/pudl \ - test/unit - -[testenv:integration] -description = Run all software integration tests and process a full year of data. -extras = - test - datasette -commands = - pytest {tty:--color=yes} {posargs} {[testenv]covargs} test/integration - -[testenv:minmax_rows] -description = Check that all outputs have the expected number of rows. -skip_install = false -recreate = true -extras = - test -commands = - pytest {tty:--color=yes} --live-dbs \ - test/validate/epacamd_eia_test.py::test_minmax_rows \ - test/validate/ferc1_test.py::test_minmax_rows \ - test/validate/eia_test.py::test_minmax_rows \ - test/validate/mcoe_test.py::test_minmax_rows_mcoe - -[testenv:validate] -description = Run all data validation tests. This requires a complete PUDL DB. -skip_install = false -recreate = true -extras = - test -commands = - pytest {tty:--color=yes} --live-dbs test/validate - -[testenv:jupyter] -description = Ensure that designated Jupyter notebooks can be executed. -skip_install = false -recreate = true -extras = - test -commands = - pytest {tty:--color=yes} --live-dbs test/integration/jupyter_notebooks_test.py - -[testenv:ci] -description = Run all continuous integration (CI) checks & generate test coverage. -skip_install = false -recreate = true -extras = - {[testenv:docs]extras} - {[testenv:integration]extras} - {[testenv:linters]extras} -commands = - coverage erase - {[testenv:linters]commands} - {[testenv:docs]commands} - {[testenv:unit]commands} - {[testenv:integration]commands} - {[testenv]covreport} - -[testenv:full_integration] -description = Run ETL and integration tests for all years and data sources. -skip_install = false -extras = - {[testenv:integration]extras} -commands = - pytest {tty:--color=yes} {posargs} {[testenv]covargs} \ - --etl-settings src/pudl/package_data/settings/etl_full.yml \ - test/integration - -[testenv:full] -description = Run all CI checks, but for all years of data. -skip_install = false -recreate = true -extras = - {[testenv:docs]extras} - {[testenv:integration]extras} - {[testenv:linters]extras} -commands = - coverage erase - {[testenv:linters]commands} - {[testenv:docs]commands} - {[testenv:unit]commands} - {[testenv:full_integration]commands} - {[testenv]covreport} - -[testenv:nuke] -description = Nuke & recreate SQLite & Parquet outputs, then run all tests and data validations against the new outputs. -skip_install = false -recreate = true -extras = - {[testenv:docs]extras} - {[testenv:integration]extras} - {[testenv:linters]extras} -commands = - coverage erase - {[testenv:linters]commands} - {[testenv:docs]commands} - {[testenv:unit]commands} - {[testenv:integration]commands} - bash -c 'rm -f tox-nuke.log' - bash -c 'coverage run --append src/pudl/ferc_to_sqlite/cli.py --logfile tox-nuke.log --clobber src/pudl/package_data/settings/etl_full.yml' - bash -c 'coverage run --append src/pudl/cli/etl.py --logfile tox-nuke.log src/pudl/package_data/settings/etl_full.yml' - pytest {tty:--color=yes} --live-dbs {posargs} {[testenv]covargs} \ - --etl-settings src/pudl/package_data/settings/etl_full.yml \ - test/integration - {[testenv:validate]commands} - {[testenv]covreport} - -########################################################################### -# Generate and save the unmapped IDs -########################################################################### -[testenv:get_unmapped_ids] -description = Make the raw FERC1 DB and generate a PUDL database with only EIA in order to generate any unmapped IDs. -skip_install = false -extras = - {[testenv:integration]extras} -commands = - pytest {tty:--color=yes} {posargs} \ - --save-unmapped-ids \ - --ignore-foreign-key-constraints \ - --etl-settings src/pudl/package_data/settings/etl_full.yml \ - test/integration/glue_test.py - -########################################################################### -# Software Package Build & Release -########################################################################### -[testenv:build] -description = Prepare Python source and binary packages for release. -basepython = python3 -skip_install = false -extras = - dev -commands = - bash -c 'rm -rf build/* dist/* src/catalystcoop.pudl.egg-info' - python -m build - -[testenv:testrelease] -description = Do a dry run of Python package release using the PyPI test server. -basepython = python3 -skip_install = false -extras = - dev -commands = - {[testenv:build]commands} - twine check dist/* - twine upload --verbose --repository testpypi --skip-existing dist/* - -[testenv:release] -description = Release the PUDL package to the production PyPI server. -basepython = python3 -skip_install = true -extras = - dev -commands = - {[testenv:build]commands} - twine check dist/* - twine upload --verbose --skip-existing dist/*