Merge development branch into the master branch (#42)

* Initialize repo packaging based on sci py cookie * Update min python and remove pre-commit dep for now * Remove copier answers * Remove 3.12 for now * Remove pypy3.9 * Allow formatting to always pass for now * Ignore pre-commit for now * fix: bring back missing .so file and remove from gitignore * chore: remove old setup.py * ci: update branch to development Updated ci and cd yaml to trigger on development branch * ci: Add built dist test step for cd * ci: publish need both steps to finish * ci: fix python version * ci: fix artifact name and action version * ci: Remove cd for pull requests * ci: fix auto versioning for pypi * chore(deps): Add all optional deps * Update README.md * Update README.md * Update docs and devcontainer * Update .gitignore * Update .gitignore * Add build/html files * chore(deps): Update smart_open to use braingeneers version * chore(deps): Pin neuraltoolkit to v0.3.1 Pinned neuraltoolkit dependency to version 0.3.1 only. @lsetiawan: From some investigation, the actual functions that are being used in the braingeneers package from neuraltoolkit hasn't changed in over a year. And the latest stable v0.3.1 was released in March 2023. So it is safe to use this specific version and minimize breakage. * Update README.md Update installation instructions * Update .devcontainer/post_create.sh Overwrite the directory in site-packages with a symbolic link to `".[all]"` Co-authored-by: Don Setiawan <[email protected]> * Update post_create.sh Remove additional comments Resolves https://github.com/braingeneers/braingeneerspy/pull/42/files/9eb851932e98a31d0cb171fd5414512d08caa057#r1355710644 * Update post_create.sh Update the wording for the comment Resolves #42 (comment) * Update post_create.sh Uninstall the pre-installed `braingeneerspy` package Resolves comment #42 (comment) * Update LICENSE Updated LICENSE to BSD-3 Resolves comment #42 (comment) * Update pyproject.toml Updated to a BSD-3 Clause license Resolves comment #42 (comment) * Update README.md Included packages in quotation marks Replaced deprecated contribution instructions with `CONTRIBUTING.md` Resolves comments #42 (comment) #42 (comment) * Update README.md Remove wheel instructions Resolves comment #42 (comment) * Update README.md Updated Optional Dependencies installation - Directly from PyPI Resolves comment #42 (comment) * ci: Rename .readthedocs.yml to .readthedocs.yaml * Remove /docs/build files Resolves comment #42 (comment) * Update README.md Remove quotation marks for Mac users comments * Update README.md Updated badges Co-authored-by: Don Setiawan <[email protected]> * Update .readthedocs.yaml Update path to conf.py Co-authored-by: Don Setiawan <[email protected]> * Update src/braingeneers/_compat/typing.py Co-authored-by: Lon Blauvelt <[email protected]> * Update pyproject.toml Remove commented `sortedcontainers` dependency Co-authored-by: Lon Blauvelt <[email protected]> * Update README.md Remove `braingeneers-smart-open` statement Resolves comment #42 (comment) * Update README.md Updated link for AWS Data Wrangler * Update README.md Add link to the `CONTRIBUTING.md` file Resolves comment #42 (comment) * Update ci.yml Remove `PyLint` Resolves comment #42 (comment) * Delete .extgitignore Resolves comment #42 (comment) * Delete src/braingeneers/_compat directory Remove the `_compat` module Part 1 of resolving comment #42 (comment) * Update test_package.py Remove the `_compat` module tests Part 2 of resolving comment #42 (comment) * Update test_package.py Remove the `_compat` module import Part 3 of resolving comment #42 (comment) * Update ci.yml Updated the `ci.yml` to allow for Python 3.12 (experimental) support Added `continue-on-error` functionality in case the experimental support fails since it is new Resolves comment #42 (comment) @lsetiawan could you review the changes that I made here? * Update ci.yml Commenting out `continue-on-error` * Update ci.yml Remove commented line * Update ci.yml Updated `python-version` to num * Update ci.yml * Update LICENSE Updated the LICENSE to MIT * Update README.md Update to include the MIT license * Update ci.yml * Update ci.yml * Update ci.yml Add `continues-on-error` * Update ci.yml Removed commented `pre-commit` section --------- Co-authored-by: Landung 'Don' Setiawan <[email protected]> Co-authored-by: Lon Blauvelt <[email protected]>
braingeneers · Oct 26, 2023 · bfaf45f · bfaf45f
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,15 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+{
+	"image":"ghcr.io/braingeneers/research:latest",
+
+	"customizations": {
+		"vscode": {
+		  "extensions": [
+			"ms-toolsai.jupyter",
+			"ms-python.python",
+			"ms-vsliveshare.vsliveshare"
+		]
+		}
+	},
+	"postCreateCommand": "sh .devcontainer/post_create.sh"
+}
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
@@ -0,0 +1,7 @@
+# For writing commands that will be executed after the container is created
+
+# Uninstalls the braingeneerspy package (pre-installed in the research Docker image) from the environment
+python3 -m pip uninstall braingeneerspy
+
+# Installs a Python package located in the current directory in editable mode and includes all optional extras specified in the [all] section of braingeneers.
+python3 -m pip install -e ".[all]"
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -0,0 +1,101 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://scientific-python-cookie.readthedocs.io/guide/intro
+
+# Quick development
+
+The fastest way to start with development is to use nox. If you don't have nox,
+you can use `pipx run nox` to run it without installing, or `pipx install nox`.
+If you don't have pipx (pip for applications), then you can install with with
+`pip install pipx` (the only case were installing an application with regular
+pip is reasonable). If you use macOS, then pipx and nox are both in brew, use
+`brew install pipx nox`.
+
+To use, run `nox`. This will lint and test using every installed version of
+Python on your system, skipping ones that are not installed. You can also run
+specific jobs:
+
+```console
+$ nox -s lint  # Lint only
+$ nox -s tests  # Python tests
+$ nox -s docs -- serve  # Build and serve the docs
+$ nox -s build  # Make an SDist and wheel
+```
+
+Nox handles everything for you, including setting up an temporary virtual
+environment for each run.
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```bash
+python3 -m venv .venv
+source ./.venv/bin/activate
+pip install -v -e .[dev]
+```
+
+If you have the
+[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you
+can instead do:
+
+```bash
+py -m venv .venv
+py -m install -v -e .[dev]
+```
+
+# Post setup
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+pip install pre-commit # or brew install pre-commit on macOS
+pre-commit install # Will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+pytest --cov=braingeneers
+```
+
+# Building docs
+
+You can build the docs using:
+
+```bash
+nox -s docs
+```
+
+You can see a preview with:
+
+```bash
+nox -s docs -- serve
+```
+
+# Pre-commit
+
+This project uses pre-commit for all style checking. While you can run it with
+nox, this is such an important tool that it deserves to be installed on its own.
+Install pre-commit and run:
+
+```bash
+pre-commit run -a
+```
+
+to check all files.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/matchers/pylint.json b/.github/matchers/pylint.json
@@ -0,0 +1,32 @@
+{
+  "problemMatcher": [
+    {
+      "severity": "warning",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): ([A-DF-Z]\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-warning"
+    },
+    {
+      "severity": "error",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): (E\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-error"
+    }
+  ]
+}
diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -0,0 +1,101 @@
+name: CD
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+      - main
+      - development
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build sdist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist
+
+      - name: Check products
+        run: pipx run twine check dist/*
+
+  test-built-dist:
+    needs: [dist]
+    name: Test built distribution
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/[email protected]
+        name: Install Python
+        with:
+          python-version: '3.10'
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+      - name: Publish to Test PyPI
+        uses: pypa/[email protected]
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+          skip-existing: true
+      - name: Check pypi packages
+        run: |
+          sleep 3
+          python -m pip install --upgrade pip
+
+          echo "=== Testing wheel file ==="
+          # Install wheel to get dependencies and check import
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre braingeneers
+          python -c "import braingeneers; print(braingeneers.__version__)"
+          echo "=== Done testing wheel file ==="
+
+          echo "=== Testing source tar file ==="
+          # Install tar gz and check import
+          python -m pip uninstall --yes braingeneers
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: braingeneers
+          python -c "import braingeneers; print(braingeneers.__version__)"
+          echo "=== Done testing source tar file ==="
+
+
+  publish:
+    needs: [dist, test-built-dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        if: startsWith(github.ref, 'refs/tags')
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,50 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+      - main
+      - development
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
+        experimental: [false, false, true]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install .[test]
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/[email protected]