Upgrade nanopub to v2.0.0

.github/workflows/build.yml

@@ -1,31 +1,31 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python application
-
+name: Run tests
 
 on: [push, pull_request]
 
 jobs:
-  build:
 
+  tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9, '3.10']
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements_dev.txt
           sudo apt-get install -y graphviz
-      - name: Create RSA key for nanopubs
+          pip install ".[test,dev]"
+
+      - name: Setup nanopub profile (including RSA keys)
         run: |
-          printf '\n' | setup_nanopub_profile --orcid_id 'https://orcid.org/0000-0000-0000-0000' --no-publish --name 'test'
+          np setup --orcid-id https://orcid.org/0000-0000-0000-0000 --no-publish --name test --newkeys
 
       - name: Lint with flake8
         run: |
@@ -34,16 +34,19 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
       - name: Test with pytest
         run: |
-          pip install pytest
           pytest --cov
+
       - name: Publish coverage to Coveralls
         env:
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        if: ${{ env.COVERALLS_REPO_TOKEN }}
         run: |
           coverage xml
           coveralls
+
       - name: Build Sphinx docs
         run: |
           cd docs

.github/workflows/pypi.yml

@@ -1,4 +1,4 @@
-name: Publish
+name: Publish to PyPI
 
 on:
   release:
@@ -8,18 +8,20 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        python setup.py bdist_wheel
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@master
+        python-version: "3.7"
+
+    - name: Install build dependencies
+      run: pip install build
+
+    - name: Build distribution
+      run: python -m build
+
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_FAIRWORKFLOWS_TOKEN }}

.gitignore

@@ -32,6 +32,7 @@ docs/apidocs
 
 env/
 venv/
+.venv/
 
 sample_output/
 .coveralls.yml

.pre-commit-config.yaml

@@ -0,0 +1,48 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: check-added-large-files
+        name: 🐘 Check for added large files
+    -   id: check-toml
+        name: ✔️  Check TOML
+    -   id: check-yaml
+        name: ✔️  Check YAML
+        args:
+        -   --unsafe
+    -   id: end-of-file-fixer
+        name: 🪚 Fix end of files
+    -   id: trailing-whitespace
+        name: ✂️  Trim trailing whitespaces
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.37.3
+    hooks:
+    -   id: pyupgrade
+        name: ⏫ Running pyupgrade
+        args:
+        - --py3-plus
+        - --keep-runtime-typing
+-   repo: https://github.com/myint/autoflake
+    rev: v1.5.3
+    hooks:
+    -   id: autoflake
+        name: ❄️  Running autoflake
+        args:
+        - --recursive
+        - --in-place
+        - --remove-all-unused-imports
+        - --remove-unused-variables
+        - --expand-star-imports
+        - --exclude
+        - __init__.py
+        - --remove-duplicate-keys
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    -   id: isort
+        name: 🔄 Formatting imports with isort (python)
+ci:
+    autofix_commit_msg: 🎨 [pre-commit.ci] Auto format from pre-commit.com hooks
+    autoupdate_commit_msg: ⬆ [pre-commit.ci] pre-commit autoupdate

CHANGELOG.md

@@ -4,6 +4,22 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2022-12-15
+
+### Added
+
+* Migrate to use `pyproject.toml` with a `hatch` build backend
+* Add pre-commit and a `.pre-commit-config.yaml` to make sure the files are properly formatted (similar to the nanopub package setup).
+
+### Modified
+
+* Update the `nanopub` dependency to 2.0.0 (no need for java anymore) and make the changes required.
+* Update rdflib dependency to v6+
+
+### Removed
+
+* Configuration files in the root folder of the repository have been removed, their configuration being now moved in the pyproject.toml: `setup.py`, ` MANIFEST.in `, `pytest.ini `, `requirements.txt`, `requirements_dev.txt`, `.flake8`, `.coveragerc`
+
 ## [0.3.0] - 2021-06-25
 
 ### Added

CONTRIBUTING.md

@@ -30,18 +30,54 @@ The sections below outline the steps in each case.
 1. (**important**) announce your plan to the rest of the community _before you start working_. This announcement should be in the form of a (new) issue;
 1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
 1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the master branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
-1. install the dependencies required to run `fairworkflows` in development:
-
-    ```bash
-    pip install -r requirements.txt
-    ```
-
+1. install dependencies (see instructions below)
+1. make your changes
 1. make sure the existing tests still work by running ``pytest``. Note that any pull requests to the fairworkflows repository on github will automatically trigger running of the test suite;
 1. check that the code is in accordance with the PEP8 style guide, by running ``flake8 . --count --show-source --statistics``,
-configuration is in `tox.ini`.
+    configuration is in `tox.ini`.
 1. add your own tests (if necessary);
 1. update or expand the documentation;
 1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the fairworkflows repository on GitHub;
 1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
 
 In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.
+
+### Install dependencies
+
+Install [Hatch](https://hatch.pypa.io), this will  automatically handle virtual environments and make sure all dependencies are installed when you run a script in the project:
+
+```bash
+pip install hatch
+```
+
+Install the depencies in a virtual environment:
+
+```bash
+hatch -v env create
+```
+
+### Development workflow
+
+Run example workflow defined in `examples/basic_workflow.py` (feel free to change this file if needed to try things in development):
+
+```bash
+hatch run example
+```
+
+Make sure the existing tests still work by running ``pytest``. Note that any pull requests to the fairworkflows repository on github will automatically trigger running of the test suite;
+
+```bash
+hatch run test
+```
+
+The code will be automatically formatted when you commit your changes using `pre-commit`. But you can also run the script to format the code yourself:
+
+```
+hatch run format
+```
+
+Check the code for errors, and if it is in accordance with the PEP8 style guide, by running `flake8` and `mypy`:
+
+```
+hatch run check
+```

README.md

@@ -1,4 +1,4 @@
-![Build Status](https://github.com/fair-workflows/fairworkflows/workflows/Python%20application/badge.svg)
+[![Build Status](https://github.com/fair-workflows/fairworkflows/actions/workflows/build.yml/badge.svg)](https://github.com/fair-workflows/fairworkflows/actions/workflows/build.yml)
 [![Documentation Status](https://readthedocs.org/projects/fairworkflows/badge/?version=latest)](https://fairworkflows.readthedocs.io/en/latest/?badge=latest)
 [![Coverage Status](https://coveralls.io/repos/github/fair-workflows/fairworkflows/badge.svg?branch=main)](https://coveralls.io/github/fair-workflows/fairworkflows?branch=main)
 [![PyPI version](https://badge.fury.io/py/fairworkflows.svg)](https://badge.fury.io/py/fairworkflows)
@@ -9,12 +9,12 @@
 
 # ```fairworkflows``` python library
 `fairworkflows` is a high-level, user-friendly python library that supports the construction,
-manipulation and publishing of FAIR scientific workflows using semantic technologies. 
+manipulation and publishing of FAIR scientific workflows using semantic technologies.
 
 ## Background
-`fairworkflows` is developed as a component of the FAIR Workbench, as part of the FAIR is FAIR project. 
+`fairworkflows` is developed as a component of the FAIR Workbench, as part of the FAIR is FAIR project.
 
-The focus is on description of workflows consisting of manual and computational steps using semantic technology, 
+The focus is on description of workflows consisting of manual and computational steps using semantic technology,
 such as the ontology described in the publication:
 
 _Celebi, R., Moreira, J. R., Hassan, A. A., Ayyar, S., Ridder, L., Kuhn, T., & Dumontier, M. (2019). Towards FAIR protocols and workflows: The OpenPREDICT case study._ [_arXiv:1911.09531._](https://arxiv.org/abs/1911.09531)
@@ -34,14 +34,15 @@ Checkout the [user documentation](https://fairworkflows.readthedocs.io/).
 
 The most recent release can be installed from the python package index using ```pip```:
 
-```
+```bash
 pip install fairworkflows
 ```
 
 To publish workflows to the nanopub server you need to setup your nanopub profile. This
 allows the nanopub server to identify you. Run the following in the terminal after installation:
-```
-setup_nanopub_profile
+
+```bash
+np setup
 ```
 This will add and store RSA keys to sign your nanopublications, publish a
 nanopublication with your name and ORCID iD to declare that you are
@@ -60,7 +61,7 @@ from fairworkflows import is_fairworkflow, is_fairstep, FairWorkflow
 
 ### Define a step for your workflow
 Mark a function as a FAIR step using the `is_fairstep` decorator.
-Use keyword arguments to semantically annotate the step. 
+Use keyword arguments to semantically annotate the step.
 In this example to provide a label and describe that this is a script task.
 ```python
 @is_fairstep(label='Addition', is_script_task=True)
@@ -69,7 +70,7 @@ def add(x: float, y: float) -> float:
     return x + y
 ```
 ### Define your workflow
-Define your workflow by calling previously defined step functions. 
+Define your workflow by calling previously defined step functions.
 Mark the function as a workflow using the `is_fairworkflow` decorator.
 ```python
 @is_fairworkflow(label='My Workflow')
@@ -107,3 +108,7 @@ It is expected that the library will soon interact with FAIR Data Points as well
 
 ## Relation to existing workflow formats/engines (e.g. CWL, WDL, Snakemake etc)
 This library is not intended to replace or compete with the hundreds of existing computational workflow formats, but rather to aid in RDF description and comparison of workflows in the most general sense of the term (including manual experiemental steps, notebooks, and so on). Steps in a FAIRWorkflow may very well be 'run this CWL workflow' or 'run this script', so such workflows are expected to sit more on a meta-level, describing the before-and-after of running one of these fully automated computational workflows as well.
+
+## Contribute
+
+If you would like to know how contribute, or learn how to run the project in development, feel free to check the documentation at [CONTRIBUTING.md](https://github.com/fair-workflows/fairworkflows/blob/main/CONTRIBUTING.md)

docs/index.rst

@@ -56,7 +56,7 @@ following in the terminal after installation:
 
 ::
 
-    setup_nanopub_profile
+    np setup
 
 This will add and store RSA keys to sign your nanopublications, publish
 a nanopublication with your name and ORCID iD to declare that you are