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Apply pre-commit to chxtools repository #31

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9dceec1
drafting pixi setup for chxtools requirements
jennmald Mar 10, 2026
9a925ce
Merge branch 'main' into pixi
jennmald Mar 19, 2026
ae17e02
add pre-commit rules from scientific python cookie cutter
jennmald Mar 19, 2026
eebcb9d
changes from pre-commit run
jennmald Mar 19, 2026
631b8e5
fix ruff formatting for xfuncs
jennmald Mar 19, 2026
1af6cb1
updates to chx_utilites, chx_wrapper, modelm and transfuncs
jennmald Apr 2, 2026
410b40b
fix linting for utils and add updated numpy calls
jennmald Apr 2, 2026
1634606
finished pre-commit refactor
jennmald Apr 3, 2026
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -81,7 +81,7 @@ docs/_build/
*.tiff
*.tif

#generated documntation files
#generated documentation files
doc/resource/api/generated/

# Enaml
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96 changes: 96 additions & 0 deletions .pre-commit-config.yaml
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ci:
autoupdate_commit_msg: "chore(deps): update pre-commit hooks"
autofix_commit_msg: "style: pre-commit fixes"
autoupdate_schedule: "quarterly"

exclude: "^({{cookiecutter\\.project_name}}|hooks/pre_gen_project.py$)"

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: "v6.0.0"
hooks:
- id: check-added-large-files
- id: check-case-conflict
- id: check-merge-conflict
- id: check-symlinks
- id: check-yaml
- id: debug-statements
- id: end-of-file-fixer
- id: mixed-line-ending
- id: name-tests-test
args: ["--pytest-test-first"]
- id: requirements-txt-fixer
- id: trailing-whitespace

- repo: https://github.com/adamchainz/blacken-docs
rev: "1.20.0"
hooks:
- id: blacken-docs
additional_dependencies: [black==24.*]

- repo: https://github.com/astral-sh/ruff-pre-commit
rev: "v0.15.6"
hooks:
- id: ruff-check
args: ["--fix", "--show-fixes"]
- id: ruff-format

- repo: https://github.com/pre-commit/pygrep-hooks
rev: "v1.10.0"
hooks:
- id: rst-backticks
- id: rst-directive-colons
- id: rst-inline-touching-normal

- repo: https://github.com/pre-commit/mirrors-mypy
rev: "v1.19.1"
hooks:
- id: mypy
files: "(src|tests|noxfile.py)"
args: []
additional_dependencies:
- click
- markdown-it-py
- pytest
- nox
- orjson
- repo-review>=0.10.6
- rich
- tomli>=2.0.2
- types-PyYAML

- repo: https://github.com/rbubley/mirrors-prettier
rev: "v3.8.1"
hooks:
- id: prettier
types_or: [yaml, markdown, html, css, scss, javascript, json]
args: [--prose-wrap=always]

- repo: https://github.com/crate-ci/typos
rev: "v1.44.0"
hooks:
- id: typos
exclude: ^Gemfile\.lock$

- repo: local
hooks:
- id: disallow-caps
name: Disallow improper capitalization
language: pygrep
entry: PyBind|Numpy|Cmake|CCache|Github|PyTest|RST|PyLint
exclude: (.pre-commit-config.yaml|docs/pages/guides/style\.md)$
- id: disallow-words
name: Disallow certain words
language: pygrep
entry: "[Ff]alsey"
exclude: .pre-commit-config.yaml$
- id: disallow-bad-permalinks
name: Disallow _ in permalinks
language: pygrep
entry: "^permalink:.*_.*"
- id: cog
name: Cog the pages
language: python
entry: cog -P -r -I ./helpers
files: "^docs/pages/guides/(packaging_compiled|docs|tasks|gha_basic).md|^copier.yml|^docs/_includes/pyproject.md"
additional_dependencies: [cogapp, cookiecutter, tomlkit]
2 changes: 1 addition & 1 deletion LICENSE
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Expand Up @@ -24,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
8 changes: 3 additions & 5 deletions README.md
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chxtools
========

Repository for data collection and analysis scripts that are useful at the
CHX beamline at NSLS-II (11-id).
# chxtools

Repository for data collection and analysis scripts that are useful at the CHX
beamline at NSLS-II (11-id).
70 changes: 35 additions & 35 deletions chxtools/X-ray_database/PhElAbsCross_Si.dat
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%Photon Photoel.
%Energy Absorb.
1.000E-03 1.567E+03
1.500E-03 5.333E+02
1.839E-03 3.071E+02
1.839E-03 3.191E+03
2.000E-03 2.775E+03
3.000E-03 9.767E+02
4.000E-03 4.514E+02
5.000E-03 2.438E+02
6.000E-03 1.458E+02
7.000E-03 9.388E+01
8.000E-03 6.379E+01
9.000E-03 4.521E+01
1.000E-02 3.315E+01
1.100E-02 2.499E+01
1.200E-02 1.928E+01
1.300E-02 1.517E+01
1.400E-02 1.213E+01
1.500E-02 9.848E+00
1.600E-02 8.096E+00
1.700E-02 6.730E+00
1.800E-02 5.651E+00
1.900E-02 4.787E+00
2.000E-02 4.089E+00
2.100E-02 3.518E+00
2.200E-02 3.048E+00
2.300E-02 2.656E+00
2.400E-02 2.328E+00
2.500E-02 2.051E+00
2.600E-02 1.815E+00
2.700E-02 1.614E+00
2.800E-02 1.440E+00
2.900E-02 1.291E+00
3.000E-02 1.161E+00
%Photon Photoel.
%Energy Absorb.
1.000E-03 1.567E+03
1.500E-03 5.333E+02
1.839E-03 3.071E+02
1.839E-03 3.191E+03
2.000E-03 2.775E+03
3.000E-03 9.767E+02
4.000E-03 4.514E+02
5.000E-03 2.438E+02
6.000E-03 1.458E+02
7.000E-03 9.388E+01
8.000E-03 6.379E+01
9.000E-03 4.521E+01
1.000E-02 3.315E+01
1.100E-02 2.499E+01
1.200E-02 1.928E+01
1.300E-02 1.517E+01
1.400E-02 1.213E+01
1.500E-02 9.848E+00
1.600E-02 8.096E+00
1.700E-02 6.730E+00
1.800E-02 5.651E+00
1.900E-02 4.787E+00
2.000E-02 4.089E+00
2.100E-02 3.518E+00
2.200E-02 3.048E+00
2.300E-02 2.656E+00
2.400E-02 2.328E+00
2.500E-02 2.051E+00
2.600E-02 1.815E+00
2.700E-02 1.614E+00
2.800E-02 1.440E+00
2.900E-02 1.291E+00
3.000E-02 1.161E+00
4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_01162017.dat
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% data from measurements 01/16/17
% manually taken for center of undulator cone
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
5.20 1.0 1.3782
5.40 1.0 1.4504
5.60 1.0 1.525
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4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_03182016.dat
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% data from measurements 03/18/16
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_03222016.dat
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% data from measurements 03/22/16
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_05272017.dat
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% data from measurements 05/27/17
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
5.199965 1.0 1.378589094103352
5.400622 1.0 1.4505010580342685
5.600828 1.0 1.5248993303989322
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4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_06062016.dat
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% data from measurements 06/06/16
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
5.199418 1.0 1.3673620139594027
5.400744 1.0 1.4390290269467232
5.600851 1.0 1.5129974379749154
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4 changes: 2 additions & 2 deletions chxtools/X-ray_database/id_CHX_IVU20_10042016.dat
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% data from measurements 10/04/16
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
% K colkumn is a placeholder!
% ID gap [mm] K E_1 [keV]
5.200081 1.0 1.3736578661340244
5.400614 1.0 1.4451752600116263
5.600811 1.0 1.5191900302629033
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2 changes: 1 addition & 1 deletion chxtools/X-ray_database/mu_Be.dat
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Expand Up @@ -500,4 +500,4 @@
29516.5 33249.5
29676.8 33285.3
29838.0 33320.4
30000.0 33354.8
30000.0 33354.8
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/mu_Si.dat
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Expand Up @@ -500,4 +500,4 @@
29516.5 3179.22
29676.8 3226.88
29838.0 3275.16
30000.0 3324.06
30000.0 3324.06
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/mu_Si3N4.dat
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Expand Up @@ -500,4 +500,4 @@
29516.5 3175.11
29676.8 3219.54
29838.0 3264.44
30000.0 3309.83
30000.0 3309.83
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Ag.dat
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Expand Up @@ -498,4 +498,4 @@
29515.5312 2.13935346E-06 1.31475204E-07
29676.1465 2.1174576E-06 1.28917975E-07
29837.6348 2.09574932E-06 1.264102E-07
30000.002 2.07426297E-06 1.23951438E-07
30000.002 2.07426297E-06 1.23951438E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Al.dat
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Expand Up @@ -499,4 +499,4 @@
29515.5312 6.20719788E-07 9.45491796E-10
29676.1465 6.14001522E-07 9.26816401E-10
29837.6348 6.07355958E-07 9.08543518E-10
30000.002 6.00782244E-07 8.90667595E-10
30000.002 6.00782244E-07 8.90667595E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Au.dat
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Expand Up @@ -498,4 +498,4 @@
29515.5312 3.67560688E-06 1.74805862E-07
29676.1465 3.63515437E-06 1.71332616E-07
29837.6348 3.59511068E-06 1.67928178E-07
30000.002 3.5555081E-06 1.6459181E-07
30000.002 3.5555081E-06 1.6459181E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Be.dat
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29515.5312 3.90868138E-07 1.0053737E-10
29676.1465 3.86648253E-07 9.98853569E-11
29837.6348 3.82474013E-07 9.92398316E-11
30000.002 3.78344794E-07 9.86006971E-11
30000.002 3.78344794E-07 9.86006971E-11
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_C.dat
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28779.6348 5.50912659E-07 1.691699E-10
29180.8066 5.35863933E-07 1.64976102E-10
29587.5723 5.21226639E-07 1.60958052E-10
30000.0059 5.06988613E-07 1.5710637E-10
30000.0059 5.06988613E-07 1.5710637E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_C_test.dat
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Expand Up @@ -497,4 +497,4 @@
28779.6348 5.50912659E-07 1.691699E-10
29180.8066 5.35863933E-07 1.64976102E-10
29587.5723 5.21226639E-07 1.60958052E-10
30000.0059 5.06988613E-07 1.5710637E-10
30000.0059 5.06988613E-07 1.5710637E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Cu.dat
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29515.5312 1.96632163E-06 3.31323164E-08
29676.1465 1.94497534E-06 3.24445217E-08
29837.6348 1.92386119E-06 3.17710409E-08
30000.002 1.90297612E-06 3.11116963E-08
30000.002 1.90297612E-06 3.11116963E-08
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_H2O.dat
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29515.5312 2.64595712E-07 1.1064933E-10
29676.1465 2.61737739E-07 1.09216497E-10
29837.6348 2.5891066E-07 1.07810774E-10
30000.002 2.56114106E-07 1.06431745E-10
30000.002 2.56114106E-07 1.06431745E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Hg.dat
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Expand Up @@ -496,4 +496,4 @@
29515.5312 2.56283852E-06 1.2784939E-07
29676.1465 2.53465032E-06 1.25311402E-07
29837.6348 2.5067452E-06 1.22823621E-07
30000.002 2.47914681E-06 1.20385522E-07
30000.002 2.47914681E-06 1.20385522E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Pd.dat
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Expand Up @@ -496,4 +496,4 @@
29515.5312 2.44286343E-06 1.43845782E-07
29676.1465 2.41790895E-06 1.4104296E-07
29837.6348 2.39320229E-06 1.38294439E-07
30000.002 2.36874689E-06 1.35599763E-07
30000.002 2.36874689E-06 1.35599763E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Pt.dat
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29515.5312 4.06940399E-06 1.90456674E-07
29676.1465 4.02460273E-06 1.86660998E-07
29837.6348 3.98025441E-06 1.82940738E-07
30000.002 3.93639448E-06 1.792951E-07
30000.002 3.93639448E-06 1.792951E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Si.dat
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29515.5312 5.54628173E-07 1.0515453E-09
29676.1465 5.48626929E-07 1.03037501E-09
29837.6348 5.42691055E-07 1.00966036E-09
30000.002 5.36819357E-07 9.89395676E-10
30000.002 5.36819357E-07 9.89395676E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_Si3N4.dat
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29515.5312 8.19071943E-07 1.0528991E-09
29676.1465 8.10216079E-07 1.03272146E-09
29837.6348 8.01456281E-07 1.01297337E-09
30000.002 7.9279107E-07 9.93649496E-10
30000.002 7.9279107E-07 9.93649496E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_SiO2.dat
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29515.5312 5.24062159E-07 5.92594085E-10
29676.1465 5.18396519E-07 5.81460435E-10
29837.6348 5.12792383E-07 5.70563152E-10
30000.002 5.07248785E-07 5.59899072E-10
30000.002 5.07248785E-07 5.59899072E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_W.dat
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29515.5312 3.68020096E-06 1.40336724E-07
29676.1465 3.64016569E-06 1.3754503E-07
29837.6348 3.60056629E-06 1.34808843E-07
30000.002 3.56139412E-06 1.32127752E-07
30000.002 3.56139412E-06 1.32127752E-07
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_diamond.dat
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29109.7539 8.60350383E-07 2.64745809E-10
29403.5273 8.4323932E-07 2.60027E-10
29700.2656 8.2646801E-07 2.55451521E-10
30000. 8.1002986E-07 2.51013349E-10
30000. 8.1002986E-07 2.51013349E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_dna.dat
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29515.5312 4.18539742E-07 2.31885511E-10
29676.1465 4.14018047E-07 2.28375624E-10
29837.6348 4.09545294E-07 2.24935751E-10
30000.002 4.05120772E-07 2.21564864E-10
30000.002 4.05120772E-07 2.21564864E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_ice.dat
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29515.5312 2.48719971E-07 1.04010363E-10
29676.1465 2.46033466E-07 1.02663503E-10
29837.6348 2.43376007E-07 1.01342129E-10
30000.002 2.40747255E-07 1.00045833E-10
30000.002 2.40747255E-07 1.00045833E-10
2 changes: 1 addition & 1 deletion chxtools/X-ray_database/n_kapton.dat
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29515.5312 3.49399869E-07 1.19084395E-10
29676.1465 3.45626404E-07 1.17802504E-10
29837.6348 3.41893781E-07 1.16542928E-10
30000.002 3.38201431E-07 1.15305286E-10
30000.002 3.38201431E-07 1.15305286E-10
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