diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6d53ba5a872..bf1a2156f9c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -57,7 +57,6 @@ repos: # MD013: line too long # MD024: Multiple headings with the same content # MD033: no inline HTML - # MD034: Bare URL used # MD041: first line in a file should be a top-level heading # MD025: single title - args: [--disable, MD013, MD024, MD025, MD033, MD034, MD041, "--"] + args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"] diff --git a/CHANGES.md b/CHANGES.md index ce06d4d19ce..00632d75db0 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -10,33 +10,33 @@ nav_order: 4 ### ๐Ÿ› Bug Fixes -- Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by @janosh in https://github.com/materialsproject/pymatgen/pull/3353 -- Fix MPMD set bug by @MichaelWolloch in https://github.com/materialsproject/pymatgen/pull/3355 -- Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by @janosh in https://github.com/materialsproject/pymatgen/pull/3362 -- Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by @chiang-yuan in https://github.com/materialsproject/pymatgen/pull/3343 +- Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by @janosh in +- Fix MPMD set bug by @MichaelWolloch in +- Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by @janosh in +- Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by @chiang-yuan in ### ๐Ÿ›  Enhancements -- Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3359 -- Breaking: New method of POTCAR validation by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3351 -- Add alias `.to_file()` for `.to()` method of structures and molecules by @QuantumChemist in https://github.com/materialsproject/pymatgen/pull/3356 +- Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion by @Andrew-S-Rosen in +- Breaking: New method of POTCAR validation by @esoteric-ephemera in +- Add alias `.to_file()` for `.to()` method of structures and molecules by @QuantumChemist in ### ๐Ÿงน House-Keeping -- Chargemol minor refactor by @janosh in https://github.com/materialsproject/pymatgen/pull/3357 -- Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by @janosh in https://github.com/materialsproject/pymatgen/pull/3360 -- Fix undiscovered tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3369 +- Chargemol minor refactor by @janosh in +- Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by @janosh in +- Fix undiscovered tests by @janosh in ### ๐Ÿฅ Package Health -- Bump min `numpy` to v1.25.0 by @janosh in https://github.com/materialsproject/pymatgen/pull/3352 +- Bump min `numpy` to v1.25.0 by @janosh in ## New Contributors -- @esoteric-ephemera made their first contribution in https://github.com/materialsproject/pymatgen/pull/3351 -- @QuantumChemist made their first contribution in https://github.com/materialsproject/pymatgen/pull/3356 +- @esoteric-ephemera made their first contribution in +- @QuantumChemist made their first contribution in -**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.9.25...v2023.10.3 +**Full Changelog**: ## v2023.9.25 diff --git a/docs/CHANGES.md b/docs/CHANGES.md index 8b8ba183a71..fec781a5bc4 100644 --- a/docs/CHANGES.md +++ b/docs/CHANGES.md @@ -10,33 +10,33 @@ nav_order: 4 ### ๐Ÿ› Bug Fixes -- Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by @janosh in https://github.com/materialsproject/pymatgen/pull/3353 -- Fix MPMD set bug by @MichaelWolloch in https://github.com/materialsproject/pymatgen/pull/3355 -- Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by @janosh in https://github.com/materialsproject/pymatgen/pull/3362 -- Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by @chiang-yuan in https://github.com/materialsproject/pymatgen/pull/3343 +- Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by @janosh in +- Fix MPMD set bug by @MichaelWolloch in +- Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by @janosh in +- Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by @chiang-yuan in ### ๐Ÿ›  Enhancements -- Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3359 -- Breaking: New method of POTCAR validation by @esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3351 -- Add alias `.to_file()` for `.to()` method of structures and molecules by @QuantumChemist in https://github.com/materialsproject/pymatgen/pull/3356 +- Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion by @Andrew-S-Rosen in +- Breaking: New method of POTCAR validation by @esoteric-ephemera in +- Add alias `.to_file()` for `.to()` method of structures and molecules by @QuantumChemist in ### ๐Ÿงน House-Keeping -- Chargemol minor refactor by @janosh in https://github.com/materialsproject/pymatgen/pull/3357 -- Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by @janosh in https://github.com/materialsproject/pymatgen/pull/3360 -- Fix undiscovered tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3369 +- Chargemol minor refactor by @janosh in +- Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by @janosh in +- Fix undiscovered tests by @janosh in ### ๐Ÿฅ Package Health -- Bump min `numpy` to v1.25.0 by @janosh in https://github.com/materialsproject/pymatgen/pull/3352 +- Bump min `numpy` to v1.25.0 by @janosh in ## New Contributors -- @esoteric-ephemera made their first contribution in https://github.com/materialsproject/pymatgen/pull/3351 -- @QuantumChemist made their first contribution in https://github.com/materialsproject/pymatgen/pull/3356 +- @esoteric-ephemera made their first contribution in +- @QuantumChemist made their first contribution in -**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.9.25...v2023.10.3 +**Full Changelog**: ## v2023.9.25 diff --git a/setup.py b/setup.py index 570fb363246..bc70822734f 100644 --- a/setup.py +++ b/setup.py @@ -106,7 +106,7 @@ "pymatgen.entries": ["*.json.gz", "*.yaml", "data/*.json"], "pymatgen.core": ["*.json"], "pymatgen": ["py.typed"], - "pymatgen.io.vasp": ["*.yaml", "*.json"], + "pymatgen.io.vasp": ["*.yaml", "*.json", "*.json.gz"], "pymatgen.io.feff": ["*.yaml"], "pymatgen.io.cp2k": ["*.yaml"], "pymatgen.io.lobster": ["lobster_basis/*.yaml"], diff --git a/tasks.py b/tasks.py index 677fe868087..07e661d330d 100644 --- a/tasks.py +++ b/tasks.py @@ -66,46 +66,6 @@ def make_doc(ctx): ctx.run("rm -rf doctrees", warn=True) -@task -def make_dash(ctx): - """Make customized doc version for Dash. - - :param ctx: - """ - ctx.run("cp docs_rst/conf-docset.py docs_rst/conf.py") - make_doc(ctx) - ctx.run("rm docs/_static/pymatgen.docset.tgz", warn=True) - ctx.run("doc2dash docs -n pymatgen -i docs/_images/pymatgen.svg -u https://pymatgen.org/") - plist = "pymatgen.docset/Contents/Info.plist" - xml = [] - with open(plist) as file: - for line in file: - xml.append(line.strip()) - if line.strip() == "": - xml.append("dashIndexFilePath") - xml.append("index.html") - with open(plist, "w") as file: - file.write("\n".join(xml)) - ctx.run('tar --exclude=".DS_Store" -cvzf pymatgen.tgz pymatgen.docset') - ctx.run("rm -r pymatgen.docset") - ctx.run("cp docs_rst/conf-normal.py docs_rst/conf.py") - - -@task -def contribute_dash(ctx, version): - make_dash(ctx) - ctx.run("cp pymatgen.tgz ../Dash-User-Contributions/docsets/pymatgen/pymatgen.tgz") - with cd("../Dash-User-Contributions/docsets/pymatgen"): - with open("docset.json") as file: - data = json.load(file) - data["version"] = version - with open("docset.json", "w") as file: - json.dump(data, file, indent=4) - ctx.run(f'git commit --no-verify -a -m "Update to v{version}"') - ctx.run("git push") - ctx.run("rm pymatgen.tgz") - - @task def submit_dash_pr(ctx, version): with cd("../Dash-User-Contributions/docsets/pymatgen"): @@ -121,20 +81,6 @@ def submit_dash_pr(ctx, version): print(response.text) -@task -def update_doc(ctx): - """ - Update the web documentation. - - :param ctx: - """ - ctx.run("cp docs_rst/conf-normal.py docs_rst/conf.py") - make_doc(ctx) - ctx.run("git add .") - ctx.run('git commit -a -m "Update docs"') - ctx.run("git push") - - @task def publish(ctx): """