Apply pre-commit to chxtools repository by jennmald · Pull Request #31 · NSLS2/chxtools

jennmald · 2026-04-03T19:51:45Z

this PR applies pre-commit to all files to this repo in an effort to refactor the repo

Copilot

Pull request overview

This PR introduces pre-commit tooling and applies automated formatting/cleanup across the repository to standardize style as part of a broader refactor effort.

Changes:

Added a .pre-commit-config.yaml and applied formatting/whitespace fixes repo-wide (Python, Markdown, Enaml, data files).
Introduced a pixi.toml workspace for reproducible base/dev environments and pre-commit tasks.
Refactored multiple Python modules for import hygiene and style consistency (notably xfuncs.py, attenuator/transfocator utilities, and pv_explorer).

Reviewed changes

Copilot reviewed 21 out of 60 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
versioneer.py	Formatting-only changes to Versioneer helper (strings, spacing).
setup.py	Formatting; still reads README via bare `open().read()`.
requirements_backup.txt	Reordered dependency line (`eiger-io`).
README.md	Converted header to Markdown `#` style and reflowed text.
pixi.toml	Added Pixi workspace + base/terminal/dev dependencies and tasks.
LICENSE	EOF/whitespace normalization.
chxtools/xfuncs.py	Large refactor/formatting; introduces a runtime error and accidental API renames.
chxtools/X-ray_database/rc_Si220.dat	EOF/whitespace normalization.
chxtools/X-ray_database/rc_Si111.dat	EOF/whitespace normalization.
chxtools/X-ray_database/rc_Ge220.dat	EOF/whitespace normalization.
chxtools/X-ray_database/rc_Ge111.dat	EOF/whitespace normalization.
chxtools/X-ray_database/PhElAbsCross_Si.dat	Whitespace normalization in tabular data/comments.
chxtools/X-ray_database/n_W.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_SiO2.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Si3N4.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Si.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Pt.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_protein.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Pd.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_nucleosome.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_mica.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_lipid.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_kapton.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_ice.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Hg.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_H2O.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_dna.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_diamond.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Cu.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_C.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_C_test.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Be.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Au.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Al.dat	EOF/whitespace normalization.
chxtools/X-ray_database/n_Ag.dat	EOF/whitespace normalization.
chxtools/X-ray_database/mu_Si3N4.dat	EOF/whitespace normalization.
chxtools/X-ray_database/mu_Si.dat	EOF/whitespace normalization.
chxtools/X-ray_database/mu_Be.dat	EOF/whitespace normalization.
chxtools/X-ray_database/id_CHX_IVU20_10042016.dat	Whitespace cleanup in header comments.
chxtools/X-ray_database/id_CHX_IVU20_06062016.dat	Whitespace cleanup in header comments.
chxtools/X-ray_database/id_CHX_IVU20_05272017.dat	Whitespace cleanup in header comments.
chxtools/X-ray_database/id_CHX_IVU20_03222016.dat	Whitespace cleanup in header comments.
chxtools/X-ray_database/id_CHX_IVU20_03182016.dat	Whitespace cleanup in header comments.
chxtools/X-ray_database/id_CHX_IVU20_01162017.dat	Whitespace cleanup in header comments.
chxtools/transfuncs.py	Import tightening + formatting; minor docstring/spelling fixes.
chxtools/pv_explorer/view.enaml	Trailing blank line removal.
chxtools/pv_explorer/run.py	Formatting and import wrapping cleanup.
chxtools/pv_explorer/model.py	Replace `import *` with explicit atom imports; formatting updates.
chxtools/pv_explorer/init.py	Quote normalization.
chxtools/plot_sid.py	Docstring + formatting cleanup; removed unused import.
chxtools/handlers.py	Formatting and string literal normalization; import cleanup.
chxtools/chx_wrapper.py	Formatting and exception handling cleanup; explicit pyepics import.
chxtools/bpm_stability.py	Formatting/refactor; introduces metadata key mismatch that will crash plotting.
chxtools/attfuncs2.py	Formatting, import cleanup, and docstring/comment normalization.
chxtools/attfuncs.py	Formatting, import cleanup, and safer comparisons; still heavy PV usage.
chxtools/_version.py	Formatting-only changes to generated Versioneer output.
chxtools/init.py	Quote normalization and minor formatting.
.pre-commit-config.yaml	Added pre-commit hook set (ruff/blacken-docs/prettier/typos/etc.).
.gitignore	Fixed spelling in comment (“documentation”).

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Copilot · 2026-04-03T19:55:50Z

chxtools/xfuncs.py

+        else:
+            (
+                print(
+                    "error: energy "
+                    + "%3.4f" % E
+                    + "[keV] out of range ("
+                    + "%3.4f" % np.min(m[:, 0] / 1000)
+                )
+                + "=<E<="
+                + "%3.4f" % np.max(m[:, 0] / 1000)
+                + "keV)"
+            )


In get_mu(), the out-of-range branch wraps a print() call in parentheses and then concatenates strings onto its return value (None). This will raise a TypeError when the energy is out of range, instead of printing the message. Build the full error string first and print it (or raise an exception) without attempting to add to the print() result.

Copilot · 2026-04-03T19:55:50Z

chxtools/bpm_stability.py

 meta_pvdict = dict(
-
-pv_Px = 'XF:11IDB-BI{XBPM:02}Fdbk:AKp-SP',
-pv_Ix = 'XF:11IDB-BI{XBPM:02}Fdbk:AKi-SP',
-pv_Dx = 'XF:11IDB-BI{XBPM:02}Fdbk:AKd-SP',
-pv_fdx= 'XF:11IDB-BI{XBPM:02}Fdbk:AEn-SP',
-pv_sklx= 'XF:11IDB-BI{XBPM:02}Fdbk:ACtrlScaleFactor-SP',
-pv_Kx = 'XF:11IDB-BI{XBPM:02}Pos:Kx-SP',
-
-pv_Py = 'XF:11IDB-BI{XBPM:02}Fdbk:BKp-SP',
-pv_Iy = 'XF:11IDB-BI{XBPM:02}Fdbk:BKi-SP',
-pv_Dy = 'XF:11IDB-BI{XBPM:02}Fdbk:BKd-SP',
-pv_fdy= 'XF:11IDB-BI{XBPM:02}Fdbk:BEn-SP',
-pv_skly= 'XF:11IDB-BI{XBPM:02}Fdbk:BCtrlScaleFactor-SP',
-pv_Ky = 'XF:11IDB-BI{XBPM:02}Pos:Ky-SP',
-
-pv_fdHz = 'XF:11IDB-BI{XBPM:02}Fdbk:delT-I',
-    )
+    pv_Px="XF:11IDB-BI{XBPM:02}Fdbk:AKp-SP",
+    pv_Ix="XF:11IDB-BI{XBPM:02}Fdbk:AKi-SP",
+    pv_Dx="XF:11IDB-BI{XBPM:02}Fdbk:AKd-SP",
+    pv_fdx="XF:11IDB-BI{XBPM:02}Fdbk:AEn-SP",
+    pv_sklx="XF:11IDB-BI{XBPM:02}Fdbk:ACtrlScaleFactor-SP",
+    pv_Kx="XF:11IDB-BI{XBPM:02}Pos:Kx-SP",
+    pv_Py="XF:11IDB-BI{XBPM:02}Fdbk:BKp-SP",
+    pv_It="XF:11IDB-BI{XBPM:02}Fdbk:BKi-SP",
+    pv_Dy="XF:11IDB-BI{XBPM:02}Fdbk:BKd-SP",
+    pv_fdy="XF:11IDB-BI{XBPM:02}Fdbk:BEn-SP",
+    pv_skly="XF:11IDB-BI{XBPM:02}Fdbk:BCtrlScaleFactor-SP",
+    pv_Ky="XF:11IDB-BI{XBPM:02}Pos:Ky-SP",
+    pv_fdHz="XF:11IDB-BI{XBPM:02}Fdbk:delT-I",
+)


meta_pvdict defines the Y integral gain key as "pv_It", but plot_posxy_fft() looks up metadata["pv_Iy"] (via "pv_I%s" % pp when pp="y"). This will cause a KeyError at runtime. Rename the dict key to pv_Iy (or update the lookup logic) so the metadata keys are consistent.

Copilot · 2026-04-03T19:55:51Z

chxtools/xfuncs.py

+def get_Game(Qz, alpha_i=0.12, E=8):
+    hlpstr = "by sof 01/12/2003   Returns the angle Gamma (out-of-plane angle in GIXD) defined in terms of Qz, the incident angle and the energy of the X-Ray beam. Type getGame(Qz [1/A], Incident Angle [deg] (default: 0.12deg) , E[keV] (default:8keV)), This function is vector compatible. Type get_Game('?') for help"
+    if Qz == "?":
+        print(hlpstr)
    else:
-        Qz=np.array(Qz);alpha_i=np.array(alpha_i);E=np.array(E)
-        lam=get_Lambda(E,'A')
-        return np.degrees(lam*Qz/(2*np.pi)-np.sin(alpha_i))
-
-def get_Qll(Ty,alpha_i=.12,d=1000,E=8):
-    hlpstr="LW 26-01-2005 Function returns the parallel wavevector transfer in GI-XPCS geometry [cm^-1]. Type: get_Qll(Ty[mm],alpha_i[deg] (default: 0.12deg), d [mm] (default: 1000mm),E[keV] (default:8keV))=>qll[cm^-1]; type get_Qll(\'?\') for help"
-    if Ty=='?':
-        print ( hlpstr)
+        Qz = np.array(Qz)
+        alpha_i = np.array(alpha_i)
+        E = np.array(E)
+        lam = get_Lambda(E, "A")
+        return np.degrees(lam * Qz / (2 * np.pi) - np.sin(alpha_i))


The public function name appears to have changed from get_Gam() to get_Game(). This is likely an accidental rename (the help string still references get_Game/getGame inconsistently) and is a breaking API change for callers importing get_Gam. Consider restoring the original name (or providing a backwards-compatible alias) and aligning the help string with the actual function name.

Copilot · 2026-04-03T19:55:51Z

chxtools/xfuncs.py

+def get_Qz(Game, alpha_i=0.12, E=8):
+    hlpstr = "function by sof 01/12/2003   Returns the Qz z-component of wavevector transfer defined in terms of the incident  and measured angles and the energy of the X-Ray beam.  Type get_Qz(Game [deg], alpha_i [deg] (default: 0.12deg), E[keV] (default: 8keV)). This function is vector compatible. Type get_Qz('?') for help."
+    if Game == "?":
+        print(hlpstr)
    else:
-        E=np.array(E);Gam=np.deg2rad(np.array(Gam));alpha_i=np.deg2rad(np.array(alpha_i))
-        lam=get_Lambda(E,'A')
-        return 2*np.pi*(np.sin(Gam)+np.sin(alpha_i))/lam
+        E = np.array(E)
+        Game = np.deg2rad(np.array(Game))
+        alpha_i = np.deg2rad(np.array(alpha_i))
+        lam = get_Lambda(E, "A")
+        return 2 * np.pi * (np.sin(Game) + np.sin(alpha_i)) / lam


Similarly, get_Qz() now takes parameter name Game instead of Gam. While positional calls still work, any keyword calls using Gam= will break, and the rename looks tied to the get_Gam/get_Game change. Consider reverting the parameter name (or supporting both via **kwargs) to preserve backwards compatibility.

Copilot · 2026-04-03T19:55:51Z

setup.py

+    author="Brookhaven National Laboratory",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
    packages=find_packages(),


setup.py reads README.md with open(...).read() without a context manager or explicit encoding. This can leave the file handle unclosed and may fail on systems with a non-UTF-8 default encoding. Prefer reading it via a context manager (and specify encoding="utf-8").

jennmald added 8 commits March 10, 2026 09:21

drafting pixi setup for chxtools requirements

9dceec1

Merge branch 'main' into pixi

9a925ce

add pre-commit rules from scientific python cookie cutter

ae17e02

changes from pre-commit run

eebcb9d

fix ruff formatting for xfuncs

631b8e5

updates to chx_utilites, chx_wrapper, modelm and transfuncs

1af6cb1

fix linting for utils and add updated numpy calls

410b40b

finished pre-commit refactor

1634606

jennmald requested review from Copilot and mrakitin April 3, 2026 19:51

Copilot started reviewing on behalf of jennmald April 3, 2026 19:52 View session

Copilot AI reviewed Apr 3, 2026

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Apply pre-commit to chxtools repository#31

Apply pre-commit to chxtools repository#31
jennmald wants to merge 8 commits intoNSLS2:mainfrom
jennmald:pre-commit

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