Devel #8
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Devel #8
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Now the PyMatgenStructureFormat doesn't support the <kbd>from_system</kbd> method. This PR adds this method, enabling users to convert the <kbd>pymatgen.core.Structure</kbd> to the dpdata format, which is convenient when you use <kbd>pymatgen.transformations</kbd> to build the atomic model. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
When downloading the source code of a branch or a release from GitHub or the mirror, there is no Git version information, making setuptools-scm unable to read the version. The alternative way is to add a git archive file supported by setuptools-scm. See: * https://setuptools-scm.readthedocs.io/en/latest/usage/#git-archives (available in setuptools-scm 7.0.0) * https://git-scm.com/docs/git-archive#Documentation/git-archive.txt-export-subst * https://docs.github.com/en/repositories/working-with-files/using-files/downloading-source-code-archives Generated by the task: njzjz-bot/njzjz-bot#4.
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](astral-sh/ruff-pre-commit@v0.3.5...v0.3.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.7 → v0.4.1](astral-sh/ruff-pre-commit@v0.3.7...v0.4.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Add function description on `system.py/check_type_map`
Fix the warning below:
```
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:6
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:6: DeprecationWarning: invalid escape sequence '\|'
latt_patt = "\|\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:7
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:7: DeprecationWarning: invalid escape sequence '\|'
pos_patt_first = "\|\s+[0-9]{1,}[:]\s\w+\s(\w+)(\s.*[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:8
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:8: DeprecationWarning: invalid escape sequence '\s'
pos_patt_other = "\s+[a][t][o][m]\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+(\w{1,2})"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:9
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:9: DeprecationWarning: invalid escape sequence '\|'
force_patt = "\|\s+[0-9]{1,}\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:10
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:10: DeprecationWarning: invalid escape sequence '\s'
eng_patt = "Total energy uncorrected.*([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+eV"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:41
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:41: DeprecationWarning: invalid escape sequence '\s'
while len(re.split("\s+", lines[blk_idx])) == 0:
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:44
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:44: DeprecationWarning: invalid escape sequence '\s'
if len(re.split("\s+", lines[blk_idx])) == 0 or lines[blk_idx] == "":
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:332
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:332: DeprecationWarning: invalid escape sequence '\s'
if len(re.split("\s+", geometry_inlines[iline])) >= 3:
```
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