docs: make docstrings and docs instrument neutral (#1125) - #1127
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Generic prose in cellreader no longer calls raw files "res-files" or cellpy files "hdf5 files" (module docstring, set_raw_datadir, set_cellpy_datadir, check_file_ids, load, one debug message). The Neware xlsx loader docstrings no longer claim to load Arbin data from MS SQL server, and the Biologic mpr loader documents a .mpr path instead of .res. Maccor header-alias comments say the alias is shared with the Arbin SQL loaders rather than "new Arbin SQL Server". Unit/summary docs phrase the Arbin Ah case as one tester among many, and basic_usage says the .res filenames are only the running example. Genuinely Arbin-specific text (drivers, arbin_res, dataset_number) is unchanged. Adds the HISTORY bullet and archives the issue-flow files. Closes #1125 Co-authored-by: Jan Petter Maehlen <jepe@ife.no>
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Closes #1125
What
Removes wording that still assumes cellpy is a
.res(Arbin) loader, while keeping every mention that is genuinely Arbin-specific.Docstrings / comments (no behaviour change)
src/cellpy/readers/cellreader.py: module docstring now says "common.cellpyformat" and points atcellpy.print_instruments(); the save example writes.cellpyinstead of.h5.set_raw_datadir,set_cellpy_datadir(its example now calls the right method),check_file_idsand the deprecatedloadno longer talk about "res-files" / "hdf5 files". Onelogging.debugstring:contains %i raw files.neware_xlsx.py: class/loader docstrings no longer claim to load "arbin-data from MS SQL server" (copy-paste leftover).biologics_mpr.py:file_nameis documented as a.mprpath, not.res.maccor_txt_one.py/maccor_txt_zero.py:# new Arbin SQL Servercomments on Maccor header aliases →# alias shared with the Arbin SQL loaders.Docs
reference/summary_columns.md: 58 columns "for a plain load from any tester"; the Ah example is introduced with "For example, with an Arbin.resfile".getting_started/basic_usage.md: one sentence that the.resfilenames are only the running example and any registered tester format works the same way.guides/units.md,fundamentals/glossary.md,agents/index.md: Arbin Ah phrased as one tester among many; "large raw files (.res, SQL dumps, …)".Kept on purpose: installation / troubleshooting /
cellpy info --checkdriver text, the instrument table,arbin_resloader ids,dataset_number,example_data.raw_file()being "a small Arbin file", config/secrets, and comparative comments inmerger/harmonize/declarations. Rendered tutorials underdocs/examples/are out of scope (they come from the notebooks).Triage inventory lives in
.issueflows/03-solved-issues/issue1125_plan.md.How to test
uv run --group docs zensical build --clean→No issues founduv run .issueflows/00-tools/check_docs_relative_links.py→ all relative links resolveMPLBACKEND=Agg uv run pytest -m essential→ 981 passed, 74 skipped; the 2 failures intests/test_filefinder.py::test_find_by_project_*fail identically on a stashedorigin/masterin the same VM (master CI is green), so they are environment-specific and unrelated.black --checkon the touched source files reports the same 3 pre-existing reformat suggestions as master.