Support recent versions of pymatgen (#39)

* added try except to_string VS to_str

* fix tests

* update flake8

* CI: separate coveralls upload to its own step

* use coveralls parallel version

* CI: add comment about coveralls

---------

Co-authored-by: Kristjan Eimre <[email protected]>

.github/workflows/build.yml

@@ -55,8 +55,23 @@ jobs:
               env:
                   # show timings of tests
                   PYTEST_ADDOPTS: --durations=0
-                  COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
               run: |
                   py.test --cov aiida_gaussian --cov-append .
-                  coveralls --service=github
+
+            # note that for a matrix test that will send multiple reports to coveralls,
+            # the parallel version should be used to avoid errors.
+            - name: Send coverage to Coveralls (parallel)
+              uses: coverallsapp/github-action@v2
+              with:
+                  parallel: true
+                  flag-name: run ${{ join(matrix.*, ' - ') }}
+
+    coveralls-finish:
+        needs: tests
+        if: ${{ always() }}
+        runs-on: ubuntu-latest
+        steps:
+            - name: Coveralls Finished
+              uses: coverallsapp/github-action@v2
+              with:
+                  parallel-finished: true

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
           - id: black
             language_version: python3
     - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
+      rev: 7.1.0
       hooks:
           - id: flake8
             args: [--count, --show-source, --statistics]

aiida_gaussian/calculations/gaussian.py

@@ -218,4 +218,7 @@ def _render_input_string_from_params(cls, parameters, pmg_structure):
         parameters.setdefault("spin_multiplicity", parameters.pop("multiplicity", None))
         parameters["title"] = "input generated by the aiida-gaussian plugin"
         gaussian_input = GaussianInput(pmg_structure, **parameters)
-        return gaussian_input.to_string(cart_coords=True)
+        try:
+            return gaussian_input.to_string(cart_coords=True)
+        except AttributeError:
+            return gaussian_input.to_str(cart_coords=True)

pyproject.toml

@@ -40,7 +40,7 @@ testing = [
     "pgtest~=1.3.2",
     "wheel~=0.31",
     "coverage",
-    "pytest~=6.1",
+    "pytest~=7.0",
     "pytest-cov",
     "pytest-regressions~=2.2",
     "coveralls",

tests/parsers/test_base.py

@@ -1,4 +1,12 @@
-"""Tests for the :class:`aiida_gaussian.parsers.gaussian.GaussianBaseParser` class."""
+"""
+Tests for the :class:`aiida_gaussian.parsers.gaussian.GaussianBaseParser` class.
+
+Note on updated parsers (e.g. in Pymatgen) and data_regression:
+If newer versions of parsers add extra fields, just update the reference data with
+    pytest --force-regen
+Although this will cause tests to fails with folder versions of the parser, but in
+general it should not be a problem.
+"""
 # pylint: disable=redefined-outer-name
 
 

tests/parsers/test_base/test_nan_inf.yml

@@ -18,8 +18,10 @@ metadata:
   - 1127102.5
   functional: M062X
   legacy_package_version: 16revisionC.02
+  memory_available: 300000000000
   methods:
   - DFT
+  num_cpu: 44
   package: Gaussian
   package_version: 2016+C.02
   platform: ES64L