chore: upgrade scaffolding (#18)

superlinear-ai · Apr 21, 2024 · 0aa00df · 0aa00df
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Showing 8 changed files with 421 additions and 383 deletions.
diff --git a/.cruft.json b/.cruft.json
@@ -1,30 +1,27 @@
 {
   "template": "https://github.com/radix-ai/poetry-cookiecutter",
-  "commit": "4127874124193c60cd5e2bfaa025473b8f30411f",
+  "commit": "8ab7ee0accff3b9cb0e470bfc925858fc04d1e97",
   "checkout": null,
   "context": {
     "cookiecutter": {
-      "package_name": "Conformal Tights",
-      "package_description": "A scikit-learn meta-estimator for computing tight conformal predictions",
-      "package_url": "https://github.com/radix-ai/conformal-tights",
+      "project_type": "package",
+      "project_name": "Conformal Tights",
+      "project_description": "A Python package that adds conformal prediction of coherent quantiles and intervals to any scikit-learn regressor or Darts forecaster.",
+      "project_url": "https://github.com/radix-ai/conformal-tights",
       "author_name": "Laurent Sorber",
       "author_email": "[email protected]",
       "python_version": "3.10",
-      "docker_image": "python:$PYTHON_VERSION-slim",
       "development_environment": "strict",
       "with_conventional_commits": "1",
       "with_fastapi_api": "0",
-      "with_jupyter_lab": "0",
-      "with_pydantic_typing": "0",
-      "with_sentry_logging": "0",
-      "with_streamlit_app": "0",
       "with_typer_cli": "0",
       "continuous_integration": "GitHub",
-      "docstring_style": "NumPy",
       "private_package_repository_name": "",
       "private_package_repository_url": "",
-      "__package_name_kebab_case": "conformal-tights",
-      "__package_name_snake_case": "conformal_tights",
+      "__docker_image": "python:$PYTHON_VERSION-slim",
+      "__docstring_style": "NumPy",
+      "__project_name_kebab_case": "conformal-tights",
+      "__project_name_snake_case": "conformal_tights",
       "_template": "https://github.com/radix-ai/poetry-cookiecutter"
     }
   },

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -10,6 +10,8 @@
         "vscode": {
             "extensions": [
                 "charliermarsh.ruff",
+                "GitHub.vscode-github-actions",
+                "GitHub.vscode-pull-request-github",
                 "ms-python.mypy-type-checker",
                 "ms-python.python",
                 "ms-toolsai.jupyter",

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -8,4 +8,22 @@ updates:
     commit-message:
       prefix: "ci"
       prefix-development: "ci"
-      include: "scope"
+      include: scope
+    groups:
+      ci-dependencies:
+        patterns:
+          - "*"
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: monthly
+    commit-message:
+      prefix: "chore"
+      prefix-development: "build"
+      include: scope
+    allow:
+      - dependency-type: development
+    versioning-strategy: increase
+    groups:
+      development-dependencies:
+        dependency-type: development
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -28,7 +28,7 @@ jobs:
           node-version: 21
 
       - name: Install @devcontainers/cli
-        run: npm install --location=global @devcontainers/cli@0.55.0
+        run: npm install --location=global @devcontainers/cli@0.58.0
 
       - name: Start Dev Container
         run: |

diff --git a/README.md b/README.md
@@ -262,10 +262,12 @@ plt.tight_layout()
 
     ```sh
     cat << EOF >> ~/.ssh/config
+
     Host *
       AddKeysToAgent yes
       IgnoreUnknown UseKeychain
       UseKeychain yes
+      ForwardAgent yes
     EOF
     ```
 
@@ -275,12 +277,12 @@ plt.tight_layout()
 <summary>2. Install Docker</summary>
 
 1. [Install Docker Desktop](https://www.docker.com/get-started).
-    - Enable *Use Docker Compose V2* in Docker Desktop's preferences window.
     - *Linux only*:
         - Export your user's user id and group id so that [files created in the Dev Container are owned by your user](https://github.com/moby/moby/issues/3206):
 
             ```sh
             cat << EOF >> ~/.bashrc
+            
             export UID=$(id --user)
             export GID=$(id --group)
             EOF

diff --git a/notebooks/README.ipynb b/notebooks/README.ipynb
@@ -9,6 +9,7 @@
                 "# 👖 Conformal Tights\n",
                 "\n",
                 "Conformal Tights is a Python package that exports:\n",
+                "\n",
                 "- a [scikit-learn](https://github.com/scikit-learn/scikit-learn) [meta-estimator](https://scikit-learn.org/stable/glossary.html#term-meta-estimator) that adds [conformal prediction](https://en.wikipedia.org/wiki/Conformal_prediction) of coherent [quantiles](https://en.wikipedia.org/wiki/Quantile) and [intervals](https://en.wikipedia.org/wiki/Prediction_interval) to any [scikit-learn regressor](https://scikit-learn.org/stable/glossary.html#term-regressor)\n",
                 "- a [Darts](https://github.com/unit8co/darts) [forecaster](https://unit8co.github.io/darts/generated_api/darts.models.forecasting.regression_model.html) that adds conformally calibrated [probabilistic time series forecasting](https://unit8co.github.io/darts/userguide/forecasting_overview.html#probabilistic-forecasts) to any scikit-learn regressor\n",
                 "\n",
@@ -65,16 +66,7 @@
                     "remove_output"
                 ]
             },
-            "outputs": [
-                {
-                    "name": "stderr",
-                    "output_type": "stream",
-                    "text": [
-                        "/opt/conformal-tights-env/lib/python3.10/site-packages/statsforecast/core.py:26: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-                        "  from tqdm.autonotebook import tqdm\n"
-                    ]
-                }
-            ],
+            "outputs": [],
             "source": [
                 "from conformal_tights import ConformalCoherentQuantileRegressor\n",
                 "from sklearn.datasets import fetch_openml\n",
@@ -608,12 +600,15 @@
                 "\n",
                 "1. [Generate an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key) and [add the SSH key to your GitHub account](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account).\n",
                 "1. Configure SSH to automatically load your SSH keys:\n",
+                "\n",
                 "    ```sh\n",
                 "    cat << EOF >> ~/.ssh/config\n",
+                "\n",
                 "    Host *\n",
                 "      AddKeysToAgent yes\n",
                 "      IgnoreUnknown UseKeychain\n",
                 "      UseKeychain yes\n",
+                "      ForwardAgent yes\n",
                 "    EOF\n",
                 "    ```\n",
                 "\n",
@@ -623,11 +618,12 @@
                 "<summary>2. Install Docker</summary>\n",
                 "\n",
                 "1. [Install Docker Desktop](https://www.docker.com/get-started).\n",
-                "    - Enable _Use Docker Compose V2_ in Docker Desktop's preferences window.\n",
-                "    - _Linux only_:\n",
+                "    - *Linux only*:\n",
                 "        - Export your user's user id and group id so that [files created in the Dev Container are owned by your user](https://github.com/moby/moby/issues/3206):\n",
+                "\n",
                 "            ```sh\n",
                 "            cat << EOF >> ~/.bashrc\n",
+                "            \n",
                 "            export UID=$(id --user)\n",
                 "            export GID=$(id --group)\n",
                 "            EOF\n",
@@ -639,7 +635,7 @@
                 "<summary>3. Install VS Code or PyCharm</summary>\n",
                 "\n",
                 "1. [Install VS Code](https://code.visualstudio.com/) and [VS Code's Dev Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers). Alternatively, install [PyCharm](https://www.jetbrains.com/pycharm/download/).\n",
-                "2. _Optional:_ install a [Nerd Font](https://www.nerdfonts.com/font-downloads) such as [FiraCode Nerd Font](https://github.com/ryanoasis/nerd-fonts/tree/master/patched-fonts/FiraCode) and [configure VS Code](https://github.com/tonsky/FiraCode/wiki/VS-Code-Instructions) or [configure PyCharm](https://github.com/tonsky/FiraCode/wiki/Intellij-products-instructions) to use it.\n",
+                "2. *Optional:* install a [Nerd Font](https://www.nerdfonts.com/font-downloads) such as [FiraCode Nerd Font](https://github.com/ryanoasis/nerd-fonts/tree/master/patched-fonts/FiraCode) and [configure VS Code](https://github.com/tonsky/FiraCode/wiki/VS-Code-Instructions) or [configure PyCharm](https://github.com/tonsky/FiraCode/wiki/Intellij-products-instructions) to use it.\n",
                 "\n",
                 "</details>\n",
                 "\n",
@@ -650,11 +646,11 @@
                 "\n",
                 "The following development environments are supported:\n",
                 "\n",
-                "1. ⭐️ _GitHub Codespaces_: click on _Code_ and select _Create codespace_ to start a Dev Container with [GitHub Codespaces](https://github.com/features/codespaces).\n",
-                "1. ⭐️ _Dev Container (with container volume)_: click on [Open in Dev Containers](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/radix-ai/conformal-tights) to clone this repository in a container volume and create a Dev Container with VS Code.\n",
-                "1. _Dev Container_: clone this repository, open it with VS Code, and run <kbd>Ctrl/⌘</kbd> + <kbd>⇧</kbd> + <kbd>P</kbd> → _Dev Containers: Reopen in Container_.\n",
-                "1. _PyCharm_: clone this repository, open it with PyCharm, and [configure Docker Compose as a remote interpreter](https://www.jetbrains.com/help/pycharm/using-docker-compose-as-a-remote-interpreter.html#docker-compose-remote) with the `dev` service.\n",
-                "1. _Terminal_: clone this repository, open it with your terminal, and run `docker compose up --detach dev` to start a Dev Container in the background, and then run `docker compose exec dev zsh` to open a shell prompt in the Dev Container.\n",
+                "1. ⭐️ *GitHub Codespaces*: click on *Code* and select *Create codespace* to start a Dev Container with [GitHub Codespaces](https://github.com/features/codespaces).\n",
+                "1. ⭐️ *Dev Container (with container volume)*: click on [Open in Dev Containers](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/radix-ai/conformal-tights) to clone this repository in a container volume and create a Dev Container with VS Code.\n",
+                "1. *Dev Container*: clone this repository, open it with VS Code, and run <kbd>Ctrl/⌘</kbd> + <kbd>⇧</kbd> + <kbd>P</kbd> → *Dev Containers: Reopen in Container*.\n",
+                "1. *PyCharm*: clone this repository, open it with PyCharm, and [configure Docker Compose as a remote interpreter](https://www.jetbrains.com/help/pycharm/using-docker-compose-as-a-remote-interpreter.html#docker-compose-remote) with the `dev` service.\n",
+                "1. *Terminal*: clone this repository, open it with your terminal, and run `docker compose up --detach dev` to start a Dev Container in the background, and then run `docker compose exec dev zsh` to open a shell prompt in the Dev Container.\n",
                 "\n",
                 "</details>\n",
                 "\n",