From 7287feb306239584c392f9686ee20c47c0f24d0a Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 09:26:10 +0200 Subject: [PATCH 01/11] bump and pin pymatgen (reason : dos fingerprints update) --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2ce0c954..a9b78dd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ classifiers = [ ] requires-python = ">=3.9,<3.13" dependencies = [ - "pymatgen>=2024.5.1", + "pymatgen>=2024.9.10", "numpy<3.0.0", "typing", ] From 62b0e495b3853f062958622e643a96e3f0b6b59a Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 09:27:18 +0200 Subject: [PATCH 02/11] adapt calc_qualtiy and fingerprints usage to latest pymatgen changes --- src/lobsterpy/cohp/analyze.py | 12 ++++++------ src/lobsterpy/featurize/core.py | 29 ++++------------------------- tests/featurize/test_batch.py | 7 ++++--- tests/featurize/test_core.py | 2 +- 4 files changed, 15 insertions(+), 35 deletions(-) diff --git a/src/lobsterpy/cohp/analyze.py b/src/lobsterpy/cohp/analyze.py index ee9be0e8..22a471c6 100644 --- a/src/lobsterpy/cohp/analyze.py +++ b/src/lobsterpy/cohp/analyze.py @@ -1693,18 +1693,18 @@ def get_lobster_calc_quality_summary( max_e=max_e, n_bins=n_bins, normalize=True, - type=orb.name, + fp_type=orb.name, ) fp_vasp_orb = dos_vasp.get_dos_fp( min_e=min_e, max_e=max_e, n_bins=n_bins, normalize=True, - type=orb.name, + fp_type=orb.name, ) tani_orb = round( - dos_vasp.get_dos_fp_similarity(fp_lobster_orb, fp_vasp_orb, tanimoto=True), + dos_vasp.get_dos_fp_similarity(fp_lobster_orb, fp_vasp_orb, metric="tanimoto"), 4, ) quality_dict["dos_comparisons"][f"tanimoto_orb_{orb.name}"] = tani_orb # type: ignore @@ -1714,17 +1714,17 @@ def get_lobster_calc_quality_summary( max_e=max_e, n_bins=n_bins, normalize=True, - type="summed_pdos", + fp_type="summed_pdos", ) fp_vasp = dos_vasp.get_dos_fp( min_e=min_e, max_e=max_e, n_bins=n_bins, normalize=True, - type="summed_pdos", + fp_type="summed_pdos", ) - tanimoto_summed = round(dos_vasp.get_dos_fp_similarity(fp_lobster, fp_vasp, tanimoto=True), 4) + tanimoto_summed = round(dos_vasp.get_dos_fp_similarity(fp_lobster, fp_vasp, metric="tanimoto"), 4) quality_dict["dos_comparisons"]["tanimoto_summed"] = tanimoto_summed # type: ignore quality_dict["dos_comparisons"]["e_range"] = [min_e, max_e] # type: ignore quality_dict["dos_comparisons"]["n_bins"] = n_bins # type: ignore diff --git a/src/lobsterpy/featurize/core.py b/src/lobsterpy/featurize/core.py index d8c20a00..0dac6646 100644 --- a/src/lobsterpy/featurize/core.py +++ b/src/lobsterpy/featurize/core.py @@ -1009,27 +1009,6 @@ def get_df(self, ids: str | None = None) -> pd.DataFrame: return df -class DosFingerprint(NamedTuple): - """ - Represents a Density of States (DOS) fingerprint. - - This named tuple is used to store information related to the Density of States (DOS) - in a material. It includes the energies, densities, type, number of bins, and bin width. - - :param energies: The energy values associated with the DOS. - :param densities: The corresponding density values for each energy. - :param type: The type of DOS fingerprint. - :param n_bins: The number of bins used in the fingerprint. - :param bin_width: The width of each bin in the DOS fingerprint. - """ - - energies: np.ndarray - densities: np.ndarray - type: str - n_bins: int - bin_width: float - - class FeaturizeDoscar: """ Class to compute DOS moments and fingerprints from DOSCAR.lobster / DOSCAR.LSO.lobster. @@ -1155,15 +1134,15 @@ def get_fingerprint_df( ids = Path(self.path_to_doscar).parent.name df = pd.DataFrame(index=[ids], columns=["DOS_FP"]) - fp = self.dos.get_dos_fp( - type=fp_type, + dos_fp = self.dos.get_dos_fp( + fp_type=fp_type, normalize=normalize, n_bins=n_bins, binning=binning, max_e=self.e_range[-1] if self.e_range is not None else None, min_e=self.e_range[0] if self.e_range is not None else None, - )._asdict() + ) - df.loc[ids, "DOS_FP"] = DosFingerprint(**fp) + df.loc[ids, "DOS_FP"] = dos_fp return df diff --git a/tests/featurize/test_batch.py b/tests/featurize/test_batch.py index c5a30f2b..bdb8fceb 100644 --- a/tests/featurize/test_batch.py +++ b/tests/featurize/test_batch.py @@ -8,8 +8,9 @@ BatchStructureGraphs, BatchSummaryFeaturizer, ) -from lobsterpy.featurize.core import CoxxFingerprint, DosFingerprint +from lobsterpy.featurize.core import CoxxFingerprint from pymatgen.analysis.graphs import StructureGraph +from pymatgen.electronic_structure.dos import DosFingerprint CurrentDir = Path(__file__).absolute().parent TestDir = CurrentDir / "../" @@ -576,7 +577,7 @@ def test_batch_dos_featurizer_non_lso(self): for dos_fp in df_fp["DOS_FP"]: assert isinstance(dos_fp, DosFingerprint) - assert dos_fp.type == "p" + assert dos_fp.fp_type == "p" assert dos_fp.n_bins == 100 def test_batch_dos_featurizer_lso(self): @@ -668,7 +669,7 @@ def test_batch_dos_featurizer_lso(self): for dos_fp in df_fp_lso["DOS_FP"]: assert isinstance(dos_fp, DosFingerprint) - assert dos_fp.type == "summed_pdos" + assert dos_fp.fp_type == "summed_pdos" assert dos_fp.n_bins == 256 diff --git a/tests/featurize/test_core.py b/tests/featurize/test_core.py index 44658df2..79b2136e 100644 --- a/tests/featurize/test_core.py +++ b/tests/featurize/test_core.py @@ -4,12 +4,12 @@ import pandas as pd import pytest from lobsterpy.featurize.core import ( - DosFingerprint, FeaturizeCharges, FeaturizeCOXX, FeaturizeDoscar, FeaturizeLobsterpy, ) +from pymatgen.electronic_structure.dos import DosFingerprint CurrentDir = Path(__file__).absolute().parent TestDir = CurrentDir / "../" From 508cada986c25be81c0b641cba1578397eff0b35 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 09:39:00 +0200 Subject: [PATCH 03/11] drop python 3.9 support --- .github/workflows/python-package.yml | 6 +++--- pyproject.toml | 3 +-- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 620ea4aa..2d309351 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -17,11 +17,11 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.9" + python-version: "3.10" cache: pip cache-dependency-path: pyproject.toml - - uses: pre-commit/action@v3.0.0 + - uses: pre-commit/action@v3.0.1 test: runs-on: ubuntu-latest @@ -31,7 +31,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] split: [1, 2, 3, 4, 5, 6] diff --git a/pyproject.toml b/pyproject.toml index a9b78dd3..214040b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,6 @@ authors = [{ name = "Janine George", email = "janine.george@bam.de" }] version = "0.4.7" classifiers = [ "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -28,7 +27,7 @@ classifiers = [ "Intended Audience :: Science/Research", "Operating System :: OS Independent", ] -requires-python = ">=3.9,<3.13" +requires-python = ">=3.10,<3.13" dependencies = [ "pymatgen>=2024.9.10", "numpy<3.0.0", From 18575e06069a61ec5bcd6d00c53bbf64923ae2b9 Mon Sep 17 00:00:00 2001 From: Aakash Ashok Naik <91958822+naik-aakash@users.noreply.github.com> Date: Wed, 11 Sep 2024 10:35:22 +0200 Subject: [PATCH 04/11] atempt pinning pytest --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 214040b1..901d3253 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,7 +46,7 @@ changelog = "https://jageo.github.io/LobsterPy/about/changelog.html" [project.optional-dependencies] featurizer = ["mendeleev==0.17.0"] dev = ["pre-commit>=2.12.1"] -tests = ["flake8", "pytest", "pytest-mock", "pytest-split", "pytest-cov", "types-setuptools"] +tests = ["flake8", "pytest==8.3.2", "pytest-mock", "pytest-split", "pytest-cov", "types-setuptools"] docs = [ "sphinx-copybutton==0.5.2", "sphinx>=5,<9", From c740d9dcd346ee64b7df06dafaf75e2f847ade33 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:15:14 +0200 Subject: [PATCH 05/11] add sleep and try debugging --- .github/workflows/python-package.yml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2d309351..56bcfa7f 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -61,9 +61,17 @@ jobs: run: | micromamba activate lobpy pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations + ls -la + find . -name ".coverage" + + - name: Sleep for 30 seconds + run: | + sleep 10 + ls -la + find . -name ".coverage" - name: Upload coverage - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-${{ matrix.split }} path: .coverage @@ -84,7 +92,7 @@ jobs: - name: Download coverage artifacts continue-on-error: true - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 - name: Run coverage continue-on-error: true From 0f91a1447113493e659a425de288ba8d5e3fe2e0 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:15:38 +0200 Subject: [PATCH 06/11] unpin pytest --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 901d3253..214040b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,7 +46,7 @@ changelog = "https://jageo.github.io/LobsterPy/about/changelog.html" [project.optional-dependencies] featurizer = ["mendeleev==0.17.0"] dev = ["pre-commit>=2.12.1"] -tests = ["flake8", "pytest==8.3.2", "pytest-mock", 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"tests/structuregraph/test_graph.py::TestGraph::test_graph_nacl_cation_anion": 4.2105081574991345, + "tests/structuregraph/test_graph.py::TestGraph::test_graph_nacl_close_fermi": 4.151408321224153, + "tests/structuregraph/test_graph.py::TestGraph::test_graph_nacl_without_add_data": 4.117549822665751 } \ No newline at end of file From 1e1fdb69d894b6d7e64f6aac136a35af895b73e8 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:20:21 +0200 Subject: [PATCH 08/11] remove sleep step and update coverage path --- .github/workflows/python-package.yml | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 56bcfa7f..071be943 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -61,20 +61,14 @@ jobs: run: | micromamba activate lobpy pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations - ls -la - find . -name ".coverage" - - - name: Sleep for 30 seconds - run: | - sleep 10 - ls -la - find . -name ".coverage" + # ls -la + # find . -name ".coverage" - name: Upload coverage uses: actions/upload-artifact@v4 with: name: coverage-${{ matrix.split }} - path: .coverage + path: ./.coverage coverage: needs: test From 0c50176ce343f320da822ebb3fa88d53644b4715 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:31:16 +0200 Subject: [PATCH 09/11] try enabling hidden files --- .github/workflows/python-package.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 071be943..84c14a96 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -68,6 +68,7 @@ jobs: uses: actions/upload-artifact@v4 with: name: coverage-${{ matrix.split }} + include-hidden-files: true path: ./.coverage coverage: From 264bcd33dcc8f2f3b432edf1708fbdf965f3c33f Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:38:47 +0200 Subject: [PATCH 10/11] rename uploaded artifacts --- .github/workflows/python-package.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 84c14a96..5fbda2a4 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -61,14 +61,13 @@ jobs: run: | micromamba activate lobpy pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations - # ls -la - # find . -name ".coverage" - name: Upload coverage uses: actions/upload-artifact@v4 with: - name: coverage-${{ matrix.split }} + name: coverage-${{ matrix.split }}-${{ matrix.python-version }} include-hidden-files: true + overwrite: false path: ./.coverage coverage: From bc11fcc8ccf51a4c95cc2279a693fd4c031611d1 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 11 Sep 2024 12:50:32 +0200 Subject: [PATCH 11/11] limit to python 3.10 version in coverage combine --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 5fbda2a4..b468c2d7 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -91,7 +91,7 @@ jobs: - name: Run coverage continue-on-error: true run: | - coverage combine coverage*/.coverage* + coverage combine coverage*/.coverage-*-3.10 coverage report --show-missing - name: Upload coverage reports to Codecov