PQAnalysis 1.2.2__tar.gz → 1.3.0__tar.gz

pqanalysis-1.3.0/.github/pull_request_template.md

@@ -0,0 +1,3 @@
+## Summary
+
+-

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.github/workflows/ci.yml

@@ -15,15 +15,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.x
+        python-version: "3.12"
+        cache: pip
 
     - name: build PQAnalysis
       run: |
-        pip install .[test]
+        python -m pip install --upgrade pip
+        python -m pip install -e ".[test]"
 
     - name: Generate coverage report
       run: |
@@ -38,4 +40,3 @@ jobs:
         fail_ci_if_error: true
         flags: unittests
         verbose: true
-

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.github/workflows/docs.yml

@@ -27,24 +27,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.12
+          cache: pip
 
       - name: Requirements
         run: |
+          sudo apt-get update
           sudo apt-get install -y python3-sphinx
-          pip install .[docs]
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[docs]"
 
       - name: Build
         run: |
-          python setup.py build_ext --inplace
           cd docs
           make clean
-          rm source/code/*
+          rm -f source/code/*
           bash autodoc.sh
           make html
           cd build/html

pqanalysis-1.3.0/.github/workflows/pr-title.yml

@@ -0,0 +1,36 @@
+name: PR Title
+
+on:
+  pull_request:
+    types:
+      - opened
+      - edited
+      - reopened
+      - synchronize
+
+permissions:
+  contents: read
+
+jobs:
+  conventional-title:
+    name: conventional-title
+    runs-on: ubuntu-latest
+    env:
+      PR_TITLE: ${{ github.event.pull_request.title }}
+    steps:
+      - name: Validate PR title
+        run: |
+          shopt -s nocasematch
+          pattern='^(feat|fix|revert|ref|refactor|perf|build|chore|ci|deps|doc|docs|style|test|tests)(\([a-z0-9._-]+\))?!?: .+'
+
+          if [[ ! "$PR_TITLE" =~ $pattern ]]; then
+            echo "PR title must follow Conventional Commits."
+            echo
+            echo "Examples:"
+            echo "  feat: add a new analysis command"
+            echo "  fix(io): handle missing trajectory data"
+            echo "  refactor: simplify trajectory parsing"
+            echo
+            echo "Allowed types: feat, fix, revert, refactor, perf, build, chore, ci, deps, docs, style, test."
+            exit 1
+          fi

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.github/workflows/pylint.yml

@@ -15,37 +15,31 @@ jobs:
 
     runs-on: ubuntu-latest
 
-    permissions: write-all      # Job-level permissions configuration starts here
+    permissions:
+      contents: read
+      pull-requests: write
 
     steps:
-    - uses: actions/checkout@master
-      with:
-        persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
-        fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+    - uses: actions/checkout@v4
 
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.x
+        python-version: "3.12"
+        cache: pip
 
     - name: build PQAnalysis
       run: |
-        pip install pylint
-        pip install pylint-django
-        pip install .
+        python -m pip install --upgrade pip
+        python -m pip install -e ".[test]"
 
     - name: Lint with pylint
       id: run_pylint
       run: |
         mkdir -p .github/.pylint_cache
         export PYLINTHOME=$(pwd)/.github/.pylint_cache
-        if ${{ github.event_name == 'pull_request' }}; then
-          pylint PQAnalysis --exit-zero --persistent n | tee pylint_output.txt
-          python .github/scripts/parse_pylint.py pylint_output.txt | tee comment.txt
-        elif ${{ github.event_name == 'push' }}; then
-          pylint PQAnalysis --exit-zero --persistent y | tee pylint_output.txt
-          python .github/scripts/parse_pylint.py pylint_output.txt | tee comment.txt
-        fi
+        pylint PQAnalysis --exit-zero --persistent n | tee pylint_output.txt
+        python .github/scripts/parse_pylint.py pylint_output.txt | tee comment.txt
 
     - name: Check if pylint score is higher than 9.75
       id: check_pylint_score
@@ -88,20 +82,3 @@ jobs:
       run: |
         cat comment.txt >> "${GITHUB_STEP_SUMMARY}"
 
-    #add changes of .github/.pylint_cache to the commit if it is based on push event
-    - name: Add .github/.pylint_cache to the commit
-      if: (github.event_name == 'push' || github.event.pull_request.merged == true) && github.ref_name != 'main'
-      run: |
-        git config --global user.email "github-actions[bot]@users.noreply.github.com"
-        git config --global user.name "github-actions[bot]"
-
-        git add .github/.pylint_cache
-        git commit -m "Add .github/.pylint_cache on push event"
-
-    - name: Push changes
-      if: github.event_name == 'push'
-      uses: ad-m/github-push-action@master
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        branch: ${{ github.ref }}
-

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.github/workflows/release.yml

@@ -5,7 +5,8 @@ on:
     tags:
       - '**'
 
-permissions: write-all
+permissions:
+  contents: read
 
 jobs:
   build:
@@ -15,18 +16,19 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: "3.12"
+        cache: pip
     - name: Install pypa/build
       run: |
-        python3 -m pip install build --user
-        python3 -m pip install twine --user
+        python3 -m pip install --upgrade pip
+        python3 -m pip install build twine
 
-    - name: Build a binary wheel and a source tarball
+    - name: Build source distribution
       run: python3 -m build --sdist
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -45,7 +47,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -67,9 +69,10 @@ jobs:
         fetch-depth: 0
 
     - name: setup python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.12'
+        cache: pip
 
     - name: build git-changelog
       run: |
@@ -81,13 +84,13 @@ jobs:
         name=$(git --no-pager tag --sort=creatordate --merged ${{ github.ref_name }} | tail -2 | head -1)
         echo "previousTag: $name"
         echo "previousTag=$name" >> $GITHUB_ENV
-        echo "::set-output name=previousTag::$name"
+        echo "previousTag=$name" >> $GITHUB_OUTPUT
 
     - name: generate new changelog
       id: generate_changelog
       run: |
         name=$(git --no-pager tag --sort=creatordate --merged ${{ github.ref_name }} | tail -2 | head -1)
-        git-changelog --sections ci,doc,feat,fix,perf,test -F "$name.." -c angular > changelog.tmp
+        git-changelog --sections :all: -F "$name.." -c angular > changelog.tmp
 
     - name: Create GitHub Release
       env:
@@ -100,7 +103,7 @@ jobs:
 
     - name: Build CHANGELOG.md
       run: |
-        git-changelog --sections ci,doc,feat,fix,perf,test -o CHANGELOG.md -c angular --in-place
+        git-changelog --sections :all: -o CHANGELOG.md -c angular --in-place
 
     - name: Add CHANGELOG.md to commit
       run: |
@@ -132,7 +135,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
@@ -170,7 +173,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-package-distributions
         path: dist/

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.gitignore

@@ -7,6 +7,7 @@ _version.py
 **/*.ipynb
 
 .github/.pylint_cache/__*
+.github/.pylint_cache/
 
 .coverage
 coverage.xml
@@ -25,3 +26,4 @@ venv.bak/
 .examples
 .mypy_cache
 .pytest_cache
+.qodo

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/.pylintrc

@@ -115,10 +115,6 @@ recursive=no
 # source root.
 source-roots=
 
-# When enabled, pylint would attempt to guess common misconfiguration and emit
-# user-friendly hints instead of false-positive error messages.
-suggestion-mode=yes
-
 # Allow loading of arbitrary C extensions. Extensions are imported into the
 # active Python interpreter and may run arbitrary code.
 unsafe-load-any-extension=no

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/CHANGELOG.md

@@ -6,6 +6,49 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 <!-- insertion marker -->
+## [v1.2.5](https://github.com/MolarVerse/PQAnalysis/releases/tag/v1.2.5) - 2025-02-12
+
+<small>[Compare with v1.2.4](https://github.com/MolarVerse/PQAnalysis/compare/v1.2.4...v1.2.5)</small>
+
+## [v1.2.4](https://github.com/MolarVerse/PQAnalysis/releases/tag/v1.2.4) - 2025-02-12
+
+<small>[Compare with v1.2.3](https://github.com/MolarVerse/PQAnalysis/compare/v1.2.3...v1.2.4)</small>
+
+## [v1.2.3](https://github.com/MolarVerse/PQAnalysis/releases/tag/v1.2.3) - 2025-02-12
+
+<small>[Compare with v1.2.2](https://github.com/MolarVerse/PQAnalysis/compare/v1.2.2...v1.2.3)</small>
+
+### Docs
+
+- deleted no-box from output docs ([75eaea6](https://github.com/MolarVerse/PQAnalysis/commit/75eaea696a6c7749ed4c77613c5486afa64a5d5d) by Josef M. Gallmetzer).
+
+### Features
+
+- add randomization option for atom positions in xyz2rst conversion ([1a1ddc5](https://github.com/MolarVerse/PQAnalysis/commit/1a1ddc5a4e5cd92e54a7d31f37175beced726d57) by Josef M. Gallmetzer).
+- add xyz2rst conversion functionality and related tests ([598473f](https://github.com/MolarVerse/PQAnalysis/commit/598473f778f4d8bc5cbbd22de43d64f2ea1d7a23) by Josef M. Gallmetzer).
+- add API function to write restart files with specified format and mode ([184061e](https://github.com/MolarVerse/PQAnalysis/commit/184061ed0d51e01bd6de8d04bf8c441e900e6cf2) by Josef M. Gallmetzer).
+
+### Bug Fixes
+
+- update restart writer to conditionally include velocities and forces in output ([bd841d9](https://github.com/MolarVerse/PQAnalysis/commit/bd841d9999b44a6b183e0ccabc5be718038ef3f5) by Josef M. Gallmetzer).
+- prevent adding box line for vacuum cells in restart file writer ([5f72088](https://github.com/MolarVerse/PQAnalysis/commit/5f72088c4179d6d68d7b62fa2fc4eccc8d31c0af) by Josef M. Gallmetzer).
+
+### Tests
+
+- add test for XYZ2RstCLI program name ([e7ee687](https://github.com/MolarVerse/PQAnalysis/commit/e7ee687425532e264d47526939c19839c4d9e868) by Josef M. Gallmetzer).
+- add test for xyz2rst conversion with no box data ([119cd75](https://github.com/MolarVerse/PQAnalysis/commit/119cd75829abe883b1bde55982d03975337bade4) by Josef M. Gallmetzer).
+
+## [v1.2.2](https://github.com/MolarVerse/PQAnalysis/releases/tag/v1.2.2) - 2025-01-07
+
+<small>[Compare with v1.2.1](https://github.com/MolarVerse/PQAnalysis/compare/v1.2.1...v1.2.2)</small>
+
+### Bug Fixes
+
+- pin setuptools to version 70.0.0 so that pytest.sh works ([1b191f8](https://github.com/MolarVerse/PQAnalysis/commit/1b191f85f70d6f1b1eff0e79b600fba454527cc4) by Josef M. Gallmetzer).
+- update setuptools dependency to latest version ([d52e3b1](https://github.com/MolarVerse/PQAnalysis/commit/d52e3b16475a5cb8a48dab4fd51f79987d0b25f7) by Josef M. Gallmetzer).
+- Replace np.in1d with np.isin for improved index matching ([cfb5391](https://github.com/MolarVerse/PQAnalysis/commit/cfb5391f76fd7fee0d31b32c8f0b6d4d41455036) by Josef M. Gallmetzer).
+- Disable iteration over AtomicSystem object ([bfb0365](https://github.com/MolarVerse/PQAnalysis/commit/bfb03650c9d902569b20409bae534b4a3fc3189f) by Josef M. Gallmetzer).
+
 ## [v1.2.1](https://github.com/MolarVerse/PQAnalysis/releases/tag/v1.2.1) - 2024-08-19
 
 <small>[Compare with v1.1.2](https://github.com/MolarVerse/PQAnalysis/compare/v1.1.2...v1.2.1)</small>

pqanalysis-1.3.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+include CHANGELOG.md
+recursive-include PQAnalysis/grammar *.lark
+include PQAnalysis/io/traj_file/process_lines.pyx

{pqanalysis-1.2.2/PQAnalysis.egg-info → pqanalysis-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PQAnalysis
-Version: 1.2.2
+Version: 1.3.0
 Summary: PQAnalysis is a python package for the analysis of PQ simulations.
 Author-email: Jakob Gamper <97gamjak@gmail.com>, "Josef M. Gallmetzer" <gallmetzer.josef@gmail.com>, "Clarissa A. Seidler" <clarissa.seidler@gmail.com>
 Project-URL: Homepage, https://github.com/MolarVerse/PQAnalysis
@@ -19,20 +19,18 @@ Requires-Dist: lark
 Requires-Dist: tqdm
 Requires-Dist: decorator
 Requires-Dist: argcomplete
-Requires-Dist: yapf
 Requires-Dist: rich-argparse
-Requires-Dist: Cython
-Requires-Dist: setuptools==70.0.0
 Provides-Extra: test
+Requires-Dist: ase; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-runner; extra == "test"
 Requires-Dist: pylint; extra == "test"
-Requires-Dist: pylint-django; extra == "test"
 Requires-Dist: coverage; extra == "test"
 Requires-Dist: docstr-coverage; extra == "test"
+Provides-Extra: dev
+Requires-Dist: yapf; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx<9,>=7; extra == "docs"
 Requires-Dist: sphinx-sitemap; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
 Requires-Dist: breathe; extra == "docs"
@@ -40,6 +38,7 @@ Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: better-apidoc; extra == "docs"
 Requires-Dist: six; extra == "docs"
 Requires-Dist: docstr-coverage; extra == "docs"
+Dynamic: license-file
 
 <img src="https://raw.githubusercontent.com/MolarVerse/PQAnalysis/main/docs/source/logo/PQAnalysis.png" width="250">
 
@@ -67,12 +66,21 @@ Clone the PQAnalysis GitHub repository and navigate into the directory:
     git clone https://github.com/MolarVerse/PQAnalysis.git
     cd PQAnalysis
 
-Install with pip:
+Install in editable mode with test dependencies:
+
+    pip install -e ".[test]"
+
+Run the test suite:
+
+    python -m pytest
 
-    pip install .
+Use squash merges for pull requests. The pull request title becomes the commit
+message on the target branch, so PR titles must follow
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/):
 
-In order to have a nice changelog strategy, please stick to [conventional commit definiton](https://www.conventionalcommits.org/en/v1.0.0-beta.4/). In order to make git accept only valid commit message please make a symlink of the git-hook template `.githooks/commit-msg`:
+    feat: add a new analysis command
+    fix(io): handle missing trajectory data
 
-    ln -s .githooks/commit-msg .git/hooks/
+The local commit hook is optional contributor feedback. Enable it with:
 
-More information on preferred and undesirable commit message will come soon...
+    git config core.hooksPath .githooks

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/PQAnalysis/__init__.py

@@ -13,6 +13,7 @@ from beartype.claw import beartype_this_package
 import PQAnalysis.config as config  # pylint: disable=consider-using-from-import
 
 from PQAnalysis.utils.custom_logging import CustomLogger
+from PQAnalysis.version import __version__
 
 __base_path__ = Path(__file__).parent
 __package_name__ = __name__

pqanalysis-1.3.0/PQAnalysis/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '1.3.0'
+__version_tuple__ = version_tuple = (1, 3, 0)
+
+__commit_id__ = commit_id = 'gcf48554da'

{pqanalysis-1.2.2 → pqanalysis-1.3.0}/PQAnalysis/analysis/rdf/rdf.py

@@ -6,6 +6,7 @@ function (RDF) is a measure of the probability density
 of finding a particle at a distance r from another particle. 
 """
 
+import itertools
 import logging
 
 # 3rd party imports
@@ -75,8 +76,8 @@ class RDF:
         traj: Trajectory | TrajectoryReader,
         reference_species: SelectionCompatible,
         target_species: SelectionCompatible,
-        use_full_atom_info: bool = False,
-        no_intra_molecular: bool = False,
+        use_full_atom_info: bool | None = False,
+        no_intra_molecular: bool | None = False,
         n_bins: PositiveInt | None = None,
         delta_r: PositiveReal | None = None,
         r_max: PositiveReal | None = None,
@@ -92,10 +93,10 @@ class RDF:
             The reference species of the RDF analysis.
         target_species : SelectionCompatible
             The target species of the RDF analysis.
-        use_full_atom_info : bool, optional
+        use_full_atom_info : bool | None, optional
             Whether to use the full atom information of the trajectory
             or not, by default None (False).
-        no_intra_molecular : bool, optional
+        no_intra_molecular : bool | None, optional
             Whether to exclude intra-molecular distances or not, by default None (False).
         n_bins : PositiveInt | None, optional
             number of bins, by default None
@@ -209,7 +210,10 @@ class RDF:
             )
 
         self.first_frame = next(self.frame_generator)
-        self.topology = traj.topology
+        if traj.topology is not None:
+            self.topology = traj.topology
+        else:
+            self.topology = self.first_frame.topology
 
         self._setup_bins(
             n_bins=n_bins,
@@ -469,7 +473,7 @@ class RDF:
         calculated from these distances.
         """
 
-        for frame in tqdm(self.frame_generator,
+        for frame in tqdm(itertools.chain([self.first_frame], self.frame_generator),
             total=self.n_frames,
             disable=not with_progress_bar):
             for i, reference_index in enumerate(self.reference_indices):
@@ -486,7 +490,7 @@ class RDF:
                     reference_position,
                     target_positions,
                     frame.cell
-                )
+                ).ravel()
 
                 self.bins += self._add_to_bins(
                     distances,
@@ -527,7 +531,10 @@ class RDF:
             The differential bins of the RDF analysis based on the spherical shell model.
         """
 
-        target_density = len(self.target_index_combinations[0])
+        if self.no_intra_molecular:
+            target_density = len(self.target_index_combinations[0])
+        else:
+            target_density = len(self.target_indices)
         target_density /= self._average_volume
 
         norm = self._norm(