v1.8.5 (#48)

FCP-INDI · Jan 15, 2024 · 9e2bab0 · 9e2bab0
2 parents aa73ce2 + 4556106
commit 9e2bab0
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diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+- package-ecosystem: github-actions  # https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+  directory: /
+  schedule:
+    interval: monthly
diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml
@@ -17,15 +17,15 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v1
       with:
-        python-version: '3.x'
+        python-version: 3.x
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install poetry
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        poetry config pypi-token.pypi "${PYPI_PASSWORD}"
+        poetry build
+        poetry publish
diff --git a/.github/workflows/test_cpac.yml b/.github/workflows/test_cpac.yml
@@ -7,7 +7,6 @@ on:
   push:
     paths-ignore:
     - README.rst
-  pull_request:
 
 jobs:
   test_cpac:
@@ -22,7 +21,7 @@ jobs:
         platform: [docker]
         tag: [latest, nightly]
         go: [1.14]
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, '3.10', 3.11, 3.12]
         singularity: [3.6.4]
 
     steps:
@@ -45,20 +44,8 @@ jobs:
     - name: Prepare Singularity cache and tmp directories
       if: ${{ matrix.platform == 'singularity' }}
       run: mkdir -p ${SINGULARITY_CACHEDIR} && mkdir -p ${SINGULARITY_TMPDIR}
-    - name: Install dependencies
-      run: |
-        sudo apt-get install libffi-dev \
-                             flawfinder \
-                             libgpgme11-dev \
-                             libseccomp-dev \
-                             squashfs-tools \
-                             libssl1.1 libssl-dev \
-                             libuuid1 uuid-dev
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
-        pip install coverage coveralls nipype
     - name: Install cpac
-      run: cd $GITHUB_WORKSPACE && pip install -e .
+      run: cd $GITHUB_WORKSPACE && pip install -e ".[dev,testing]"
     - name: Test cpac, platform and tag specified
       run: |
         coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
@@ -81,12 +68,12 @@ jobs:
     - name: Report coverage
       uses: AndreMiras/coveralls-python-action@v20201129
       with:
-        parallel: True
+        parallel: true
         flag-name: Test cpac ${{ matrix.platform }} with Python ${{ matrix.python }}
       continue-on-error: true
   finalize_coverage-report:
-    needs: 
-      - test_cpac
+    needs:
+    - test_cpac
     runs-on: ubuntu-latest
     steps:
     - name: Finalize coverage report
@@ -97,7 +84,7 @@ jobs:
   update_README:
     # Only update README if tests succeed
     needs:
-      - test_cpac
+    - test_cpac
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,57 @@
+fail_fast: false
+
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.8
+  hooks:
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.4.1
+  hooks:
+  - id: mypy
+    additional_dependencies:
+    - types-tabulate
+    - types-PyYAML
+    args: [--python-version=3.8, --ignore-missing-imports]
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.11.0
+  hooks:
+  - id: pretty-format-yaml
+    args:
+    - --autofix
+    - --indent=2
+  - id: pretty-format-toml
+    exclude: ^poetry.lock$
+    args:
+    - --autofix
+    - --indent=2
+    - --no-sort
+
+- repo: https://github.com/python-poetry/poetry
+  rev: 1.6.0
+  hooks:
+  - id: poetry-check
+  - id: poetry-lock
+    args: [--no-update]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+  - id: check-case-conflict
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+    args:
+    - --fix=lf
+  - id: trailing-whitespace
+  - id: pretty-format-json
+    args:
+    - --autofix
+    - --indent=4
+    - --no-sort-keys
+  - id: check-merge-conflict
+  - id: check-yaml
+  - id: check-json
+  - id: check-toml
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,11 +1,17 @@
 =========
 Changelog
 =========
-`Version 0.6.0: Support for C-PAC v1.8.5 <https://github.com/FCP-INDI/cpac/releases/tag/v0.6.0>`_
-===============
+
+`Version 1.8.5: Support for C-PAC v1.8.5 <https://github.com/FCP-INDI/cpac/releases/tag/v1.8.5>`_
+=====================================================================================================
+
+* Changes versioning scheme to match supported C-PAC version
 * Handles relocation of default pipeline in C-PAC 1.8.5
 * Fixes a bug preventing default bindings in Mac OS ≥ 10.15
 * Replaces ``setup.cfg`` with ``pyproject.toml``
+* Replaces ``setuptools`` with ``poetry``
+* Adds pre-commit hooks for linting and formatting
+* Require Python ≥ 3.8
 
 `Version 0.5.0: Parse Resources <https://github.com/FCP-INDI/cpac/releases/tag/v0.5.0>`_
 ========================================================================================
@@ -50,11 +56,11 @@ Changelog
 ========================================================================
 * 📚 Update the main usage string to better articulate functionality
 * 📢🐳 Provide a clearer error message if package cannot connect to Docker.
-* 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4>` where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash`` 
-* 🚑 Fix some installation issues: 
+* 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4>` where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash``
+* 🚑 Fix some installation issues:
    * All required packages are now installed with ``pip install cpac``
    * Version is now set correctly
-* 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4>`_ where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash`` 
+* 🐳 Fix a bug introduced in `v0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4>`_ where some crashfiles would print for ``cpac --platform singularity crash`` but not for ``cpac --platform docker crash``
 * 🔬 Set `coverage reports <http://coveralls.io/github/shnizzedy/cpac>`_ to report local paths
 
 `Version 0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4>`_

diff --git a/README.rst b/README.rst
@@ -10,12 +10,16 @@ A Python package that wraps `C-PAC <http://fcp-indi.github.io>`_, enabling users
 Description
 ===========
 
-C-PAC Python Package is a lightweight Python package that handles interfacing a user's machine and a C-PAC container through a command line interface.
+cpac Python Package is a lightweight Python package that handles interfacing a user's machine and a C-PAC container through a command line interface.
+
+.. admonition:: Note about cpac versioning
+
+    This package's versioning scheme changed in version 1.8.5 to match C-PAC's versioning. From cpac v1.8.5 forward, the version of cpac indicates the newest supported version of C-PAC.
 
 Dependencies
 ============
 
-* `Python <https://www.python.org>`_ ≥3.7
+* `Python <https://www.python.org>`_ ≥ 3.8
 * `pip <https://pip.pypa.io>`_
 * At least one of:
 
@@ -86,6 +90,8 @@ Usage
         enter (bash, shell)
                             Enter a new C-PAC container via BASH.
         parse-resources (parse_resources)
+                            .
+                            
                             When provided with a `callback.log` file, this utility can sort through
                             the memory `runtime` usage, `estimate`, and associated `efficiency`, to
                             identify the `n` tasks with the `highest` or `lowest` of each of these
@@ -145,4 +151,3 @@ Usage
 .. |upload| image:: https://github.com/FCP-INDI/cpac/workflows/Upload%20Python%20Package/badge.svg
     :target: https://pypi.org/project/cpac/
     :alt: upload Python package to PyPI
-