PQAnalysis 1.1.2__tar.gz → 1.2__tar.gz

{pqanalysis-1.1.2 → pqanalysis-1.2}/.github/workflows/docs.yml

@@ -35,27 +35,13 @@ jobs:
           python-version: 3.12
 
       - name: Requirements
-        run: sudo apt-get install -y python3-sphinx
-          && pip3 install sphinx-rtd-theme
-          && pip3 install breathe
-          && pip3 install sphinx-sitemap
-          && pip3 install myst-parser
-          && pip3 install beartype
-          && pip3 install decorator
-          && pip3 install numpy
-          && pip3 install scipy
-          && pip3 install multimethod
-          && pip3 install lark
-          && pip3 install tqdm
-          && pip3 install argcomplete
-          && pip3 install yapf
-          && pip3 install rich-argparse
-          && pip3 install better-apidoc
-          && pip3 install six
-          && pip3 install .
+        run: |
+          sudo apt-get install -y python3-sphinx
+          pip install .[docs]
 
       - name: Build
         run: |
+          python setup.py build_ext --inplace
           cd docs
           make clean
           rm source/code/*

{pqanalysis-1.1.2 → pqanalysis-1.2}/.github/workflows/pylint.yml

@@ -47,9 +47,6 @@ jobs:
           python .github/scripts/parse_pylint.py pylint_output.txt | tee comment.txt
         fi
 
-
-    #check if the first line of comment.txt rates higher than 9.75 with following format
-    #Your code has been rated at 9.86/10 (previous run: 7.63/10, +2.22)
     - name: Check if pylint score is higher than 9.75
       id: check_pylint_score
       run: |
@@ -57,10 +54,10 @@ jobs:
         head -n3 comment.txt | tail -n 1 | awk '{print $7}'
         head -n3 comment.txt | tail -n 1 | awk '{print $7}' | cut -d '/' -f 1
         score=$(head -n3 comment.txt | tail -n 1 | awk '{print $7}' | cut -d '/' -f 1)
-        if (( $(echo "$score > 9.5" | bc -l) )); then
-          echo "Pylint score is higher than 9.5 and is $score"
+        if (( $(echo "$score > 9.75" | bc -l) )); then
+          echo "Pylint score is higher than 9.75 and is $score"
         else
-          echo "Pylint score is lower than 9.5 and is $score"
+          echo "Pylint score is lower than 9.75 and is $score"
           exit 1
         fi
       shell: bash

{pqanalysis-1.1.2 → pqanalysis-1.2}/.github/workflows/release.yml

@@ -22,10 +22,9 @@ jobs:
       run: |
         python3 -m pip install build --user
         python3 -m pip install twine --user
-        python3 -m pip install wheel --user
 
     - name: Build a binary wheel and a source tarball
-      run: python3 -m build
+      run: python3 -m build --sdist
     - name: Store the distribution packages
       uses: actions/upload-artifact@v3
       with:
@@ -88,8 +87,9 @@ jobs:
       id: generate_changelog
       run: |
         name=$(git --no-pager tag --sort=creatordate --merged ${{ github.ref_name }} | tail -2 | head -1)
-        changelog=$(git-changelog --sections ci,doc,feat,fix,perf,test -F "$name.." -c angular)"
-        echo "changelog=$changelog" >> $GITHUB_OUTPUT
+        changelog=$(git-changelog --sections ci,doc,feat,fix,perf,test -F "$name.." -c angular)
+        echo "changelog_var=$changelog" >> $GITHUB_ENV
+        echo "::set-output name=changelog_var::$changelog"
 
     - name: Create GitHub Release
       env:
@@ -98,7 +98,7 @@ jobs:
         gh release create
         '${{ github.ref_name }}'
         --repo '${{ github.repository }}'
-        --notes '${{ steps.generate_changelog.outputs.changelog }}'
+        --notes "${{ steps.generate_changelog.outputs.changelog_var }}"
 
     - name: Build CHANGELOG.md
       run: |
@@ -144,7 +144,6 @@ jobs:
       with:
         inputs: >-
           ./dist/*.tar.gz
-          ./dist/*.whl
 
     - name: Upload artifact signatures to GitHub Release
       env:

{pqanalysis-1.1.2/PQAnalysis.egg-info → pqanalysis-1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PQAnalysis
-Version: 1.1.2
+Version: 1.2
 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
@@ -21,18 +21,22 @@ Requires-Dist: decorator
 Requires-Dist: argcomplete
 Requires-Dist: yapf
 Requires-Dist: rich-argparse
+Requires-Dist: Cython
+Requires-Dist: setuptools
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
-Requires-Dist: coverage; 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: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-sitemap; extra == "docs"
-Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: breathe; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: better-apidoc; extra == "docs"
 Requires-Dist: six; extra == "docs"
 Requires-Dist: docstr-coverage; extra == "docs"

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/__init__.py

@@ -21,7 +21,6 @@ __package_name__ = __name__
 # BEARTYPE SETUP #
 ##################
 
-# TODO: change the default level to "RELEASE" after all changes are implemented
 __beartype_default_level__ = "RELEASE"
 __beartype_level__ = os.getenv(
     "PQANALYSIS_BEARTYPE_LEVEL", __beartype_default_level__

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.1.2'
-__version_tuple__ = version_tuple = (1, 1, 2)
+__version__ = version = '1.2'
+__version_tuple__ = version_tuple = (1, 2)

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/atomic_system/_decorators.py

@@ -17,7 +17,6 @@ check_atom_number_setters
     of atoms is equal to the number of positions.
 """
 
-import sys
 import numpy as np
 
 from beartype.typing import Any

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/core/api.py

@@ -17,7 +17,7 @@ def distance(
     pos1: Np1DNumberArray | Np2DNumberArray,
     pos2: Np1DNumberArray | Np2DNumberArray,
     cell: _cell.Cell = _cell.Cell(),
-    **kwargs
+    **kwargs  # pylint: disable=unused-argument
 ) -> PositiveReal | Np1DNumberArray | Np2DNumberArray:
     """
     Returns the distances between all combinations of two position arrays.
@@ -66,7 +66,7 @@ def distance(
     cell : Cell, optional
         The unit cell of the system. Default is Cell().
     **kwargs
-        Arbitrary keyword arguments.
+        Additional keyword arguments.
 
     Returns
     -------

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/gen_file/gen_file_reader.py

@@ -93,6 +93,7 @@ class GenFileReader(BaseReader):
         """
         n_atoms, periodicity = header[0].split()
         n_atoms = int(n_atoms)
+        is_periodic = False  # Default value
 
         if periodicity.lower() == "c":
             is_periodic = False

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/input_file_reader/input_file_parser.py

@@ -79,6 +79,9 @@ class InputFileParser(BaseReader):
         InputDictionary: InputDictionary
             The parsed input file dictionary.
         """
+
+        grammar_file = None  # to avoid linter warning
+
         if self.input_format == InputFileFormat.PQANALYSIS:
             grammar_file = "inputGrammar.lark"
         elif self.input_format in [InputFileFormat.PQ, InputFileFormat.QMCFC]:

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/input_file_reader/pq/output_files.py

@@ -2,8 +2,6 @@
 A module containing a Mixin class for output files of a PQ input file.
 """
 
-from PQAnalysis.exceptions import PQKeyError
-
 
 
 class _OutputFileMixin:

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/nep/nep_writer.py

@@ -316,6 +316,8 @@ class NEPWriter(BaseWriter):
 
                 self.is_validation = False
 
+                file_to_write = None  # to avoid linting warning
+
                 if j in train_indices:
                     self.n_train_frames += 1
                     file_to_write = self.train_file
@@ -339,7 +341,11 @@ class NEPWriter(BaseWriter):
                     )
 
                 self.write_from_atomic_system(
-                    system, file_to_write, use_forces, use_stress, use_virial
+                    system,
+                    file_to_write,
+                    use_forces,
+                    use_stress,
+                    use_virial,
                 )
 
                 if self.is_validation:
@@ -437,12 +443,16 @@ class NEPWriter(BaseWriter):
                 exception=NEPError
             )
 
+        n_train = 0.0
+        n_validation = 0.0
+        n_test = 0.0
+
         if total_ratios is not None:
             ratios = total_ratios.split(":")
             if len(ratios) == 2:
                 n_train = float(ratios[0])
                 n_test = float(ratios[1])
-                n_validation = 0
+                n_validation = 0.0
             elif len(ratios) == 3:
                 n_train = float(ratios[0])
                 n_test = float(ratios[1])
@@ -456,10 +466,6 @@ class NEPWriter(BaseWriter):
                     ),
                     exception=NEPError
                 )
-        else:
-            n_train = 0.0
-            n_validation = 0.0
-            n_test = 0.0
 
         sum_frames = n_train + n_test + n_validation
 

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/topology_file/topology_file_reader.py

@@ -209,6 +209,11 @@ class TopologyFileReader(BaseReader):
 
             line, comment = self._get_data_line_comment(line)
 
+            index = None  # to avoid linter warning
+            target_index = None  # to avoid linter warning
+            bond_type = None  # to avoid linter warning
+            is_linker = None  # to avoid linter warning
+
             if len(line.split()) == 4:
                 index, target_index, bond_type, _ = line.split()
                 is_linker = True
@@ -263,6 +268,12 @@ class TopologyFileReader(BaseReader):
 
             line, comment = self._get_data_line_comment(line)
 
+            index1 = None  # to avoid linter warning
+            index2 = None  # to avoid linter warning
+            index3 = None  # to avoid linter warning
+            angle_type = None  # to avoid linter warning
+            is_linker = None  # to avoid linter warning
+
             if len(line.split()) == 5:
                 index1, index2, index3, angle_type, _ = line.split()
                 is_linker = True
@@ -318,6 +329,13 @@ class TopologyFileReader(BaseReader):
 
             line, comment = self._get_data_line_comment(line)
 
+            index1 = None  # to avoid linter warning
+            index2 = None  # to avoid linter warning
+            index3 = None  # to avoid linter warning
+            index4 = None  # to avoid linter warning
+            dihedral_type = None  # to avoid linter warning
+            is_linker = None  # to avoid linter warning
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -374,6 +392,13 @@ class TopologyFileReader(BaseReader):
 
             line, comment = self._get_data_line_comment(line)
 
+            index1 = None  # to avoid linter warning
+            index2 = None  # to avoid linter warning
+            index3 = None  # to avoid linter warning
+            index4 = None  # to avoid linter warning
+            dihedral_type = None  # to avoid linter warning
+            is_linker = None  # to avoid linter warning
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -431,6 +456,11 @@ class TopologyFileReader(BaseReader):
 
             line, comment = self._get_data_line_comment(line)
 
+            index = None  # to avoid linter warning
+            target_index = None  # to avoid linter warning
+            distance = None  # to avoid linter warning
+            is_linker = None  # to avoid linter warning
+
             if len(line.split()) == 4:
                 index, target_index, distance, _ = line.split()
                 is_linker = True

pqanalysis-1.2/PQAnalysis/io/traj_file/.gitignore

@@ -0,0 +1,2 @@
+*.so
+process_lines.c

{pqanalysis-1.1.2 → pqanalysis-1.2}/PQAnalysis/io/traj_file/frame_reader.py

@@ -17,6 +17,7 @@ from PQAnalysis.utils.custom_logging import setup_logger
 from PQAnalysis import __package_name__
 
 from .exceptions import FrameReaderError
+from .process_lines import process_lines_with_atoms  # pylint: disable=import-error
 
 
 
@@ -98,7 +99,7 @@ class _FrameReader:
 
         # This should never happen - only for safety
         self.logger.error(
-            f'Invalid TrajectoryFormat given.{traj_format=}',
+            f'Invalid TrajectoryFormat given. {traj_format=}',
             exception=FrameReaderError
         )
 
@@ -315,6 +316,9 @@ class _FrameReader:
             If the header line is not valid. Either it contains too many or too few values.
         """
 
+        n_atoms = 0  # default value
+        cell = None  # default value
+
         header_line = header_line.split()
 
         if len(header_line) == 4:
@@ -364,15 +368,7 @@ class _FrameReader:
             If the given string does not contain the correct number of lines.
         """
         try:
-            # Pre-allocate xyz and atoms
-            xyz = np.empty((n_atoms, 3), dtype=np.float32)
-            atoms = [None] * n_atoms
-
-            # Fill xyz and atoms in a single loop
-            for i, line in enumerate(splitted_frame_string[2:2 + n_atoms]):
-                split_line = line.split()
-                atoms[i] = split_line[0]
-                xyz[i] = split_line[1:4]
+            atoms, xyz = process_lines_with_atoms(splitted_frame_string[2:], n_atoms)
 
             return xyz, atoms
         except ValueError: