CHANGELOG.md

Changelog

v0.10.7 (2024-04-16)

Fix

• ci: Use token to upload to TestPyPI
• The spectra glob emcee progress to False

Docs

• Correct tutorials using pymc with cov_matrix
• Fix prenspire tutorial
• Fix prtecan tutorial
• Fix LMfit tutorial
• Fix LMfit tutorial

Build

• update ruff requirement from <=0.3.6 to <=0.3.7 (#544)
• update commitizen requirement from <=3.21.3 to <=3.22.0 (#543)
• update ruff requirement from <=0.3.5 to <=0.3.6 (#542)
• update pandas requirement from <=2.2.1 to <=2.2.2 (#541)
• update sphinx-autodoc-typehints requirement from <=2.0.0 to <=2.0.1 (#540)
• docs: Update to the official upload-artifact action
• style: Fix few ruff linting errors
• Drop python 3.9; add 3.12
• update scipy requirement from <=1.12.0 to <=1.13.0
• update arviz requirement from <=0.17.1 to <=0.18.0 (#537)
• update lmfit requirement from <=1.2.2 to <=1.3.0 (#536)
• update matplotlib requirement from <=3.8.3 to <=3.8.4 (#535)
• bump codecov/codecov-action from 4.1.1 to 4.2.0 (#534)
• update ruff requirement from <=0.3.4 to <=0.3.5 (#532)
• update commitizen requirement from <=3.20.0 to <=3.21.3 (#530)
• bump actions/configure-pages from 4 to 5 (#529)

Refactor

• build: Adopt pydoclint and drop darglint
• build: From black to ruff format; tutorials

chore

• update pre-commit hooks (#545)
• update pre-commit hooks (#538)
• update pre-commit hooks (#531)

v0.10.6 (2024-03-28)

Fix

• ci: Add codecov token
• commitizen version v3.13.0 from 3.12.0
• avoid warnings from some pytest

Docs

• Adopt github-pages-deploy-action

Build

• bump codecov/codecov-action from 4.1.0 to 4.1.1 (#528)
• update pre-commit requirement from <=3.6.2 to <=3.7.0 (#526)
• update ruff requirement from <=0.3.3 to <=0.3.4 (#525)
• update commitizen requirement from <=3.18.4 to <=3.20.0 (#524)
• update ruff requirement from <=0.3.2 to <=0.3.3 (#522)
• update pandas-stubs requirement (#521)
• update coverage[toml] requirement from <=7.4.3 to <=7.4.4 (#520)
• update commitizen requirement from <=3.18.3 to <=3.18.4 (#519)
• update arviz requirement from <=0.17.0 to <=0.17.1 (#518)
• bump hatch from 1.9.3 to 1.9.4 in /.github/workflows (#516)
• update commitizen requirement from <=3.18.0 to <=3.18.3 (#515)
• update mypy requirement from <=1.8.0 to <=1.9.0 (#514)
• update pytest requirement from <=8.1.0 to <=8.1.1 (#513)
• update ruff requirement from <=0.3.1 to <=0.3.2 (#512)
• update sphinxcontrib-plantuml requirement from <=0.28 to <=0.29 (#511)
• update commitizen requirement from <=3.17.0 to <=3.18.0 (#510)
• update ruff requirement from <=0.3.0 to <=0.3.1 (#509)
• update commitizen requirement from <=3.16.0 to <=3.17.0 (#508)
• update pytest requirement from <=8.0.2 to <=8.1.0 (#507)
• update ruff requirement from <=0.2.2 to <=0.3.0 (#506)
• bump codecov/codecov-action from 4.0.2 to 4.1.0 (#505)
• update commitizen requirement from <=3.15.0 to <=3.16.0 (#504)
• bump codecov/codecov-action from 4.0.1 to 4.0.2 (#503)
• update pytest requirement from <=8.0.1 to <=8.0.2 (#502)
• update pandas requirement from <=2.2.0 to <=2.2.1 (#501)
• update coverage[toml] requirement from <=7.4.2 to <=7.4.3 (#500)
• update sphinxcontrib-plantuml requirement from <=0.27 to <=0.28 (#499)
• update coverage[toml] requirement from <=7.4.1 to <=7.4.2 (#498)
• update ruff requirement from <=0.2.1 to <=0.2.2 (#496)
• update pytest requirement from <=8.0.0 to <=8.0.1 (#495)
• update pre-commit requirement from <=3.6.1 to <=3.6.2 (#494)
• update commitizen requirement from <=3.14.1 to <=3.15.0 (#493)
• update pandas-stubs requirement (#492)
• update matplotlib requirement from <=3.8.2 to <=3.8.3 (#491)
• update tqdm requirement from <=4.66.1 to <=4.66.2 (#489)
• update pre-commit requirement from <=3.6.0 to <=3.6.1 (#488)
• update sphinx-autodoc-typehints requirement (#487)
• update ruff requirement from <=0.2.0 to <=0.2.1 (#486)
• update numpy requirement from <=1.26.3 to <=1.26.4 (#485)
• bump pip from 23.3.2 to 24.0 in /.github/workflows (#484)
• update commitizen requirement from <=3.14.0 to <=3.14.1 (#483)
• bump codecov/codecov-action from 3.1.6 to 4.0.1 (#482)
• update commitizen requirement from <=3.13.0 to <=3.14.0 (#480)
• update ruff requirement from <=0.1.15 to <=0.2.0 (#481)
• bump codecov/codecov-action from 3.1.5 to 3.1.6 (#478)
• update xdoctest requirement from <=1.1.2 to <=1.1.3 (#477)
• update ruff requirement from <=0.1.14 to <=0.1.15 (#476)
• update pytest requirement from <=7.4.4 to <=8.0.0 (#475)
• update coverage[toml] requirement from <=7.4.0 to <=7.4.1 (#474)
• update sphinx-autodoc-typehints requirement (#473)
• bump codecov/codecov-action from 3.1.4 to 3.1.5 (#472)
• update seaborn requirement from <=0.13.1 to <=0.13.2 (#471)
• bump hatch from 1.9.2 to 1.9.3 in /.github/workflows (#470)
• bump hatch from 1.9.1 to 1.9.2 in /.github/workflows (#469)
• update pandas requirement from <=2.1.4 to <=2.2.0 (#467)
• update ruff requirement from <=0.1.13 to <=0.1.14 (#468)
• update scipy requirement from <=1.11.4 to <=1.12.0 (#466)
• update pydata-sphinx-theme requirement from <=0.15.1 to <=0.15.2 (#465)
• update ruff requirement from <=0.1.12 to <=0.1.13 (#464)
• update ruff requirement from <=0.1.11 to <=0.1.12 (#463)
• update autodocsumm requirement from <=0.2.11 to <=0.2.12 (#462)
• update pydata-sphinx-theme requirement from <=0.14.4 to <=0.15.1 (#461)
• update numpy requirement from <=1.26.2 to <=1.26.3 (#460)
• update ruff requirement from <=0.1.9 to <=0.1.11 (#459)
• update seaborn requirement from <=0.13.0 to <=0.13.1 (#458)
• update pytest requirement from <=7.4.3 to <=7.4.4 (#457)
• update arviz requirement from <=0.16.1 to <=0.17.0 (#456)
• update coverage[toml] requirement from <=7.3.4 to <=7.4.0 (#455)
• update pandas-stubs requirement (#454)
• bump hatch from 1.9.0 to 1.9.1 in /.github/workflows (#453)
• update ruff requirement from <=0.1.8 to <=0.1.9 (#452)
• update mypy requirement from <=1.7.1 to <=1.8.0 (#451)
• update coverage[toml] requirement from <=7.3.3 to <=7.3.4 (#450)
• bump hatch from 1.8.1 to 1.9.0 in /.github/workflows (#446)
• update pandas-stubs requirement (#445)
• bump pip from 23.3.1 to 23.3.2 in /.github/workflows (#444)
• bump actions/download-artifact from 3 to 4 (#443)
• update coverage[toml] requirement from <=7.3.2 to <=7.3.3 (#442)
• bump hatch from 1.8.0 to 1.8.1 in /.github/workflows (#441)
• update ruff requirement from <=0.1.7 to <=0.1.8 (#440)
• bump hatch from 1.7.0 to 1.8.0 in /.github/workflows (#439)
• update pandas requirement from <=2.1.3 to <=2.1.4 (#438)
• update pre-commit requirement from <=3.5.0 to <=3.6.0 (#437)
• bump actions/setup-python from 4 to 5 (#436)
• bump actions/deploy-pages from 2 to 3 (#435)
• bump actions/configure-pages from 2 to 4 (#434)
• update ruff requirement from <=0.1.6 to <=0.1.7 (#433)
• update mypy requirement from <=1.7 to <=1.7.1 (#432)
• update commitizen requirement from <3.12.1 to <3.13.1
• bump pydata-sphinx-theme from 0.14.3 to 0.14.4 (#429)
• update pygments requirement from <2.17.2 to <2.17.3 (#428)
• bump sphinx-click from 5.0.1 to 5.1.0 (#427)
• update pygments requirement from <2.16.2 to <2.17.2 (#425)
• bump ruff from 0.1.5 to 0.1.6 (#424)
• update matplotlib requirement from <3.8.2 to <3.8.3 (#423)
• update scipy requirement from <1.11.4 to <1.11.5 (#422)
• update numpy requirement from <1.26.2 to <1.26.3 (#420)
• bump sphinx-autodoc-typehints from 1.25.0 to 1.25.2 (#419)
• update mypy requirement from <1.7 to <1.8 (#418)
• update pandas requirement from <2.1.3 to <2.1.4 (#417)
• bump sphinx-autodoc-typehints from 1.24.1 to 1.25.0 (#416)
• bump ruff from 0.1.4 to 0.1.5 (#415)
• bump ruff from 0.1.3 to 0.1.4 (#413)
• bump sphinx-autodoc-typehints from 1.24.0 to 1.24.1 (#412)
• update matplotlib requirement from <3.8.1 to <3.8.2 (#411)
• bump sphinxcontrib-plantuml from 0.26 to 0.27 (#410)
• bump pydata-sphinx-theme from 0.14.2 to 0.14.3 (#409)
• update pandas requirement from <2.1.2 to <2.1.3 (#407)
• bump ruff from 0.1.2 to 0.1.3 (#406)
• update xdoctest requirement from <1.1.2 to <1.1.3 (#405)
• bump pydata-sphinx-theme from 0.14.1 to 0.14.2 (#404)
• bump ruff from 0.1.1 to 0.1.2 (#403)
• update pytest requirement from <7.4.3 to <7.4.4 (#402)
• bump pip from 23.3 to 23.3.1 in /.github/workflows (#400)
• update commitizen requirement from <3.10.2 to <3.12.1 (#398)
• bump ruff from 0.1.0 to 0.1.1 (#399)
• bump ruff from 0.0.292 to 0.1.0 (#397)
• bump pip from 23.2.1 to 23.3 in /.github/workflows (#395)
• bump pre-commit from 3.4.0 to 3.5.0 (#394)
• update numpy requirement from <1.26.1 to <1.26.2 (#393)
• update commitizen requirement from <3.10.1 to <3.10.2 (#392)
• update mypy requirement from <1.6 to <1.7 (#391)
• update coverage[toml] requirement from <7.3.2 to <7.3.3 (#388)
• bump ruff from 0.0.291 to 0.0.292 (#387)
• update seaborn requirement from <0.12.3 to <0.13.1 (#386)
• bump pandas-stubs from 2.0.3.230814 to 2.1.1.230928 (#385)
• update scipy requirement from <1.11.3 to <1.11.4 (#384)
• bump ruff from 0.0.290 to 0.0.291 (#382)
• update commitizen requirement from <3.9.1 to <3.10.1 (#381)
• update pandas requirement from <2.1.1 to <2.1.2 (#380)
• bump pydata-sphinx-theme from 0.14.0 to 0.14.1 (#379)

CI/CD

• Sync dependabot update time
• Docs from gh actions

Refactor

• build: Run pre-commit autoupdate

chore

• update pre-commit hooks (#527)
• update pre-commit hooks (#523)
• update pre-commit hooks (#517)
• update pre-commit hooks (#497)
• update pre-commit hooks (#490)
• update pre-commit hooks (#426)
• update pre-commit hooks (#421)
• update pre-commit hooks (#414)
• update pre-commit hooks (#408)
• update pre-commit hooks (#401)
• update pre-commit hooks (#396)
• update pre-commit hooks (#390)
• update pre-commit hooks (#389)
• update pre-commit hooks (#383)
• update pre-commit hooks (#378)

v0.10.5 (2023-09-18)

Docs

• Improve README.md

Build

• update matplotlib requirement from <3.7.4 to <3.8.1
• update numpy requirement from <1.25.3 to <1.26.1 (#377)
• bump pydata-sphinx-theme from 0.13.3 to 0.14.0 (#376)
• update commitizen requirement from <3.8.3 to <3.9.1 (#374)
• bump ruff from 0.0.289 to 0.0.290 (#373)
• bump sphinx from 7.2.5 to 7.2.6 (#372)
• bump ruff from 0.0.288 to 0.0.289 (#371)
• bump ruff from 0.0.287 to 0.0.288 (#369)
• update matplotlib requirement from <3.7.3 to <3.7.4 (#368)
• update commitizen requirement from <3.8.1 to <3.8.3 (#367)

Refactor

• Fix type annotations of matplotlib-3.8.1

chore

• update pre-commit hooks (#370)

v0.10.4 (2023-09-08)

Fix

• Remove insane min=0 for S0

Docs

• Fix readme usage instruction

Test

• Fix test_fit_titration_glob missing a parametrized condition test

Build

• update pytest requirement from <7.4.2 to <7.4.3 (#366)

v0.10.3 (2023-09-07)

Fix

• note_to_csv: Ensure unix EOL

Docs

• Add usage instruction for ppr enspire and note_to_csv

Test

• For note_to_csv

Build

• update coverage[toml] requirement from <7.3.1 to <7.3.2 (#365)
• update commitizen requirement from <3.7.2 to <3.8.1 (#364)

v0.10.2 (2023-09-05)

Fix

• docs: click cli

Build

• bump actions/checkout from 3 to 4 (#363)
• update commitizen requirement from <3.7.1 to <3.7.2 (#361)
• bump pre-commit from 3.3.3 to 3.4.0 (#360)
• bump ruff from 0.0.286 to 0.0.287 (#359)
• update pytest requirement from <7.4.1 to <7.4.2 (#358)
• update pandas requirement from <2.0.4 to <2.1.1 (#357)
• bump sphinx from 7.2.4 to 7.2.5 (#356)
• bump sphinx from 7.2.3 to 7.2.4 (#354)
• update commitizen requirement from <3.6.1 to <3.7.1 (#353)
• bump sphinxcontrib-plantuml from 0.25 to 0.26 (#352)
• bump nbsphinx from 0.9.2 to 0.9.3 (#351)
• bump ruff from 0.0.285 to 0.0.286 (#350)
• bump sphinx from 7.2.2 to 7.2.3 (#349)
• bump sphinx-click from 4.4.0 to 5.0.1 (#346)
• update click requirement from <8.1.7 to <8.1.8 (#347)
• bump ruff from 0.0.284 to 0.0.285 (#345)
• update scipy requirement from <1.11.2 to <1.11.3 (#344)
• bump sphinx from 7.1.2 to 7.2.2 (#343)

chore

• update pre-commit hooks (#362)
• update pre-commit hooks (#355)
• update pre-commit hooks (#348)

v0.10.1 (2023-08-16)

Fix

• (#342)
• pd.Index generic (#341)
• Refactor to accommodate ruff update to 0.0.280

Docs

• Add pdf to RtD
• Add all formats to RtD

Build

• bump pandas-stubs from 2.0.2.230605 to 2.0.3.230814
• bump pandas-stubs from 2.0.2.230605 to 2.0.3.230814
• update coverage[toml] requirement from <7.2.8 to <7.3.1 (#340)
• update mypy requirement from <1.5 to <1.6 (#339)
• update tqdm requirement from <4.65.3 to <4.66.2 (#338)
• bump ruff from 0.0.283 to 0.0.284 (#337)
• update tqdm requirement from <4.65.1 to <4.65.3 (#335)
• bump ruff from 0.0.282 to 0.0.283 (#334)
• update pygments requirement from <2.15.2 to <2.16.2 (#332)
• prettier --prose-wrap=preserve
• bump sphinx from 7.1.1 to 7.1.2 (#331)
• bump ruff from 0.0.281 to 0.0.282 (#330)
• update commitizen requirement from <3.5.5 to <3.6.1 (#327)
• update numpy requirement from <1.25.2 to <1.25.3 (#328)
• bump ruff from 0.0.280 to 0.0.281 (#326)
• update commitizen requirement from <3.5.4 to <3.5.5 (#325)
• bump sphinx from 7.0.1 to 7.1.1 (#324)
• bump pip from 23.2 to 23.2.1 in /.github/workflows (#321)
• bump ruff from 0.0.278 to 0.0.280 (#320)
• bump sphinx-autodoc-typehints from 1.23.3 to 1.24.0 (#319)
• update click requirement from <8.1.6 to <8.1.7 (#318)

chore

• update pre-commit hooks
• update pre-commit hooks
• update pre-commit hooks (#333)
• ruff 0.281 keys() refactor
• update pre-commit hooks
• update pre-commit hooks

v0.10.0 (2023-07-19)

Feat

• Add spec to fit-titration dropping fit_titration_old
• Add fit-titration glob dropping fit_titration_glob_old

Docs

• Update ipynb

Test

• Update coverage run

Build

• update arviz requirement from <0.16.1 to <0.16.2 (#317)
• bump pre-commit from 3.0.1 to 3.3.3 (#315)
• Eliminate pip-deepfreeze
• Relocate 'docs' from 'envs.docs.scripts' to 'default.scripts'
• Relocate coverage into tests
• Relocate 'lint' from 'envs.lint.scripts' to 'default.scripts'
• bump pip from 23.1.2 to 23.2 in /.github/workflows (#314)
• update commitizen requirement from <3.5.3 to <3.5.4 (#313)
• Eliminate dependency on typeguard

Refactor

• Simplify plot_emcee fix options in fit-titration glob
• Reorganize fit-titration glob test data files
• Add FitKwargs into TitrationAnalysis to streamline fit() method
• Remove type ignore in PlateScheme also add PlateScheme test

chore

• update pre-commit hooks (#316)

v0.9.1 (2023-07-15)

Docs

• Fix zenodo badge to auto-update

Refactor

• Remove silencer noqa for merge_md and norm metadata

v0.9.0 (2023-07-15)

Feat

• Change tecan and enspire as subcommands of ppr
• pr.tecan exports png for each well
• prtecan: new fit; sort results; add export_png
• New glob-emcee fitting; add note_to_csv

Fix

• plots of critical cl fit
• tit_cl K>epsilon; refactor is_ph as Titration attribute
• fit_tecan in main cli

Docs

• Update tutorials and (partially) UML
• Update zotero DOI
• Add click doc for note_to_csv

Build

• update click requirement from <8.1.5 to <8.1.6 (#311)
• update lmfit requirement from <1.2.2 to <1.2.3 (#312)
• update arviz requirement from <0.15.2 to <0.16.1 (#310)
• bump ruff from 0.0.277 to 0.0.278 (#309)
• bump actions/upload-pages-artifact from 1 to 2 (#308)
• update numpy requirement from <1.25.1 to <1.25.2 (#306)
• update click requirement from <8.1.4 to <8.1.5 (#304)
• update matplotlib requirement from <3.7.2 to <3.7.3 (#303)
• bump ruff from 0.0.275 to 0.0.277 (#301)

Refactor

• Rename TitrationAnalysis.results and .result_dfs
• Use is_ph instead of kind
• Removes confint
• cli: pr.tecan and pr.enspire
• Drop py3.8

chore

• Remove redundant NaN filtering
• update pre-commit hooks (#307)
• update pre-commit hooks (#300)

v0.8.1 (2023-07-03)

Docs

• fix pointer to changelog in project.toml (#274)

Build

• update pandas requirement from <2.0.3 to <2.0.4 (#297)
• update scipy requirement from <1.11.1 to <1.11.2 (#296)
• bump sphinx-autodoc-typehints from 1.23.2 to 1.23.3 (#294)
• update pytest requirement from <7.3.3 to <7.4.1 (#292)
• update commitizen requirement from <3.3.1 to <3.5.3 (#291)
• update scipy requirement from <1.10.2 to <1.11.1 (#293)
• bump ruff from 0.0.272 to 0.0.275 (#289)
• update mypy requirement from <1.4 to <1.5 (#286)
• update numpy requirement from <1.24.4 to <1.25.1 (#284)
• bump sphinx-autodoc-typehints from 1.23.0 to 1.23.2 (#283)
• update commitizen requirement from <3.2.3 to <3.3.1 (#281)
• update pytest requirement from <7.3.2 to <7.3.3 (#279)
• bump ruff from 0.0.270 to 0.0.272 (#278)
• bump pandas-stubs from 2.0.1.230501 to 2.0.2.230605 (#276)

Refactor

• docs: Drop rpy; convert into LMfit.ipynb

chore

• update pre-commit hooks (#295)
• update pre-commit hooks (#285)
• update pre-commit hooks (#280)
• update pre-commit hooks (#275)

v0.8.0 (2023-06-05)

Feat

• prenspire: build and fit single-and-global SVD-or-band titrations
• clop: fit_titration for old note
• clop: fit titration global old and fit titration old as cli command
• add __version__ for output into "Meas-{version}"

Test

• clop: add test for new fit_titration cli

Docs

• Add instruction to install auto completion

Build

• remove pygrep-hook: python-check-blanket-noqa and python-no-eval
• update coverage[toml] requirement from <7.2.7 to <7.2.8 (#272)
• update pandas requirement from <2.0.2 to <2.0.3 (#271)
• bump nbsphinx from 0.9.1 to 0.9.2 (#269)
• bump ruff from 0.0.269 to 0.0.270 (#268)
• update coverage[toml] requirement from <7.2.6 to <7.2.7 (#267)
• update rpy2 requirement from <3.5.12 to <3.5.13 (#265)
• bump ruff from 0.0.267 to 0.0.269 (#264)

Refactor

• prenspire: new Note (titration build) and fit_titration cmd; keep the old ExpNote for compatibility with old note files.
• prenspire: analyze_spectra_glob for SVD or multiple bands
• prenspire: SVD spectra expand (with helpers functions) on old fit_titration script

chore

• update pre-commit hooks (#270)
• update pre-commit hooks (#266)

v0.7.1 (2023-05-18)

Fix

• docs: README links to pages

Docs

• Enhance the alignment between the changelog and tags

Build

• bump codecov/codecov-action from 3.1.3 to 3.1.4 (#262)

Refactor

• enspire: Adopt dataclass with helper functions

chore

• update pre-commit hooks (#261)

v0.7.0 (2023-05-15)

Feat

• prtecan: Typecheck PlateScheme and improve docs

Test

• Refactor fixtures for prtecan

Build

• bump ruff from 0.0.265 to 0.0.267 (#259)
• bump sphinx from 7.0.0 to 7.0.1 (#258)
• bump typeguard from 4.0.0rc6 to 4.0.0 (#257)

v0.6.0 (2023-05-12)

Feat

• prenspire: Read platemap othen than 96-well

Build

• update commitizen requirement from <3.2.2 to <3.2.3 (#256)

v0.5.4 (2023-05-11)

Docs

• Reorganize readme sphinx etc.

Build

• update mypy requirement from <1.3 to <1.4 (#253)
• update sympy requirement from <1.11.2 to <1.13.0 (#251)

v0.5.3 (2023-05-09)

Docs

• updated docs/README.md

v0.5.2 (2023-05-09)

CI/CD

• Unify CI/CD into a single workflow

v0.5.1 (2023-05-09)

Fix

• CI/CD: release to PyPI

v0.5.0 (2023-05-09)

Feat

• Add prenspire to parse PerkinElmer files

Build

• bump ruff from 0.0.264 to 0.0.265 (#246)
• bump typeguard from 4.0.0rc5 to 4.0.0rc6 (#245)
• update commitizen requirement from <3.2.1 to <3.2.2 (#244)

chore

• update pre-commit hooks (#247)
• default to python 3.11

v0.4.10 (2023-05-03)

Refactor

• Labelblock KEYS

v0.4.9 (2023-05-03)

Build

• bump sphinx from 6.2.1 to 7.0.0 (#236)
• bump ruff from 0.0.263 to 0.0.264 (#243)
• bump autodocsumm from 0.2.10 to 0.2.11 (#242)
• update lmfit requirement from <1.2.1 to <1.2.2 (#241)

Refactor

• update typeguard to 4.0.0rc5

v0.4.8 (2023-05-02)

Docs

• Lint README.md with markdownlint-cli

Build

• update lmfit requirement from <1.1.1 to <1.2.1 (#213)
• remove pyupgrade as ruff "UP" fully replaces it
• bump pandas-stubs from 2.0.0.230412 to 2.0.1.230501 (#240)
• update commitizen requirement from <3.1.1 to <3.2.1 (#239)
• update coverage[toml] requirement from <7.2.4 to <7.2.6 (#238)
• bump pip from 23.1.1 to 23.1.2 in /.github/workflows (#235)
• update commitizen requirement from <2.42.2 to <3.1.1 (#234)
• bump sphinx from 6.1.3 to 6.2.1 (#233)
• bump ruff from 0.0.262 to 0.0.263 (#232)
• update pandas requirement from <2.0.1 to <2.0.2 (#231)
• bump pip from 23.1 to 23.1.1 in /.github/workflows (#229)
• update numpy requirement from <1.24.3 to <1.24.4 (#227)
• bump codecov/codecov-action from 3.1.2 to 3.1.3 (#225)
• update corner requirement from <2.2.2 to <2.2.3 (#211)
• update pygments requirement from <2.14.1 to <2.15.2 (#223)
• bump pip from 23.0.1 to 23.1 in /.github/workflows (#222)
• update pytest requirement from <7.2.3 to <7.3.2 (#220)
• bump pandas-stubs from 1.5.3.230321 to 2.0.0.230412 (#218)
• bump ruff from 0.0.260 to 0.0.262 (#224)
• update rpy2 requirement from <3.5.11 to <3.5.12 (#221)
• bump sphinx-autodoc-typehints from 1.22 to 1.23.0 (#219)
• bump codecov/codecov-action from 3.1.1 to 3.1.2 (#217)
• bump pip-deepfreeze from 1.1.0 to 1.2.0 in /.github/workflows (#216)
• update mypy requirement from <1.2 to <1.3 (#210)
• update coverage[toml] requirement from <7.2.3 to <7.2.4 (#209)
• bump hatch from 1.6.3 to 1.7.0 in /.github/workflows (#207)
• update pandas requirement from <1.5.4 to <2.0.1 (#205)
• bump pydata-sphinx-theme from 0.13.1 to 0.13.3 (#204)
• bump ruff from 0.0.259 to 0.0.260 (#203)
• bump ruff from 0.0.258 to 0.0.259 (#201)
• bump ruff from 0.0.257 to 0.0.258 (#199)
• bump pandas-stubs from 1.5.3.230304 to 1.5.3.230321 (#198)

CI/CD

• skip tests when only docs are changed

chore

• update pre-commit hooks (#230)
• update pre-commit hooks (#214)
• update pre-commit hooks (#206)

v0.4.7 (2023-03-21)

Docs

• Update Readme

Build

• docs: fix RTD

v0.4.6 (2023-03-21)

Style

• yaml with prettier through apheleia

Build

• bump actions/deploy-pages from 1 to 2 (#196)
• update coverage[toml] requirement from <7.2.2 to <7.2.3 (#193)
• bump nbsphinx from 0.8.12 to 0.9.1 (#191)
• update openpyxl requirement from <3.1.2 to <3.1.3 (#189)
• bump myst-parser from 0.19.1 to 1.0.0 (#187)
• update mypy requirement from <1.1 to <1.2 (#186)
• bump pydata-sphinx-theme from 0.13.0 to 0.13.1 (#185)
• bump pandas-stubs from 1.5.3.230227 to 1.5.3.230304 (#184)
• update rpy2 requirement from <3.5.10 to <3.5.11 (#183)
• update tqdm requirement from <4.64.2 to <4.65.1 (#182)
• update pytest requirement from <7.2.2 to <7.2.3 (#181)
• bump sphinxcontrib-plantuml from 0.24.1 to 0.25 (#180)
• update matplotlib requirement from <3.7.1 to <3.7.2 (#179)
• bump myst-parser from 0.18.1 to 0.19.1 (#178)
• bump pydata-sphinx-theme from 0.12.0 to 0.13.0 (#176)
• bump pandas-stubs from 1.5.3.230214 to 1.5.3.230227 (#175)
• update rpy2 requirement from <3.5.9 to <3.5.10 (#174)
• update coverage[toml] requirement from <7.2.1 to <7.2.2 (#173)
• update commitizen requirement from <2.42.1 to <2.42.2 (#172)
• update coverage[toml] requirement from <7.1.1 to <7.2.1 (#171)
• bump pip from 23.0 to 23.0.1 in /.github/workflows (#170)
• update scipy requirement from <1.10.1 to <1.10.2 (#169)
• bump pandas-stubs from 1.5.3.230203 to 1.5.3.230214 (#168)
• update openpyxl requirement from <3.1.1 to <3.1.2 (#167)
• update matplotlib requirement from <3.6.4 to <3.7.1 (#166)
• bump pip-deepfreeze from 1.0.0 to 1.1.0 in /.github/workflows (#165)
• update commitizen requirement from <2.41.1 to <2.42.1 (#164)
• style: more pre-commit checks and formatting
• update commitizen requirement from <2.40.1 to <2.41.1
• update mypy requirement from <0.992 to <1.1 (#162)
• pylsp-ruff,mypy as dev deps
• lint: updt
• update rpy2 requirement from <3.5.8 to <3.5.9 (#160)
• bump pandas-stubs from 1.5.2.230105 to 1.5.3.230203 (#159)
• update numpy requirement from <1.24.2 to <1.24.3 (#158)

Refactor

• build: pre-commit autoupdate
• remove unneeded symbols in prtecan.__all__
• separate fitting from prtecan and define __all__

chore

• update pre-commit hooks (#197)

v0.4.5 (2023-02-03)

Fix

• docs update

v0.4.4 (2023-02-03)

Fix

• docs: emcee sections

v0.4.3 (2023-02-03)

Build

• update ipykernel requirement from <6.20.3 to <6.21.2 (#156)
• docs: use stable-python 3.11; update docs and style cleaning

v0.4.2 (2023-02-01)

Fix

• CD testpypi

v0.4.1 (2023-02-01)

Fix

• docs: CI badge

Docs

• venv with hatch and pre-commit init instruction

Build

• bumping lmfit from 1.0.3 to 1.1.0
• update xdoctest requirement from <1.1.1 to <1.1.2 (#155)
• update openpyxl requirement from <3.0.11 to <3.1.1 (#154)
• update ipython requirement from <8.8.1 to <8.9.1 (#152)
• update emcee requirement from <3.1.4 to <3.1.5 (#151)
• bump pip from 22.3.1 to 23.0 in /.github/workflows (#148)
• dropped pip-df
• deps: bump numpy 1.24.1

v0.4.0 (2023-01-30)

Feat

• build: ruff (#144)

v0.3.20 (2023-01-28)

Build

• bump jupyter-client from 7.4.9 to 8.0.1 (#143)

CI/CD

• fix rtd and sudden lint failing isort installation

v0.3.19 (2023-01-28)

Fix

• build and rtd

v0.3.18 (2023-01-28)

CI/CD

• fix CD publish

v0.3.17 (2023-01-28)

Fix

• mypy after updates

Style

• pyproject deps and updates

Build

• commitizen: pre-commit autoupdate
• ci: dropped nox and pdm in favor of hatch (#141)
• bump websocket-client from 1.4.2 to 1.5.0 (#140)
• bump nbclassic from 0.4.8 to 0.5.1 (#139)
• bump jupyter-client from 7.4.8 to 8.0.1 (#138)
• bump prometheus-client from 0.15.0 to 0.16.0 (#130)
• bump sphinxcontrib-applehelp from 1.0.2 to 1.0.4 (#129)
• bump jupyter-core from 5.1.0 to 5.1.5 (#134)
• bump nbconvert from 7.2.6 to 7.2.9 (#136)
• bump debugpy from 1.6.4 to 1.6.6 (#131)
• bump sphinx-autodoc-typehints from 1.21.1 to 1.21.8 (#135)
• bump commitizen from 2.39.1 to 2.40.0 (#127)
• bump bleach from 5.0.1 to 6.0.0 (#128)
• bump nbsphinx from 0.8.11 to 0.8.12 (#125)
• bump coverage from 7.0.5 to 7.1.0 (#137)
• bump pandas from 1.5.2 to 1.5.3 (#123)
• bump markupsafe from 2.1.1 to 2.1.2 (#118)

v0.3.16 (2023-01-16)

Fix

• clop --version after click updates (#68)

Style

• correct few typos (#69)

v0.3.15 (2023-01-13)

Refactor

• tests and src for pylint
• py3.11: include py3.11 in supported versions

v0.3.14 (2023-01-01)

CI/CD

• fix CD

v0.3.13 (2022-12-30)

Style

• prettify .yml and .md files

Build

• deps: pdm update
• pre-commit: autoupdate prettier isort cz pdm shellcheck
• cz: to bump and generate changelog

CI/CD

• automating CD
• test cleaning workflows

v0.3.12 (2022-12-13)

CI Changes

• Drop poetry in favor of PDM.
• Taken inspiration from scikit-hep.
• PDM, pre-commit and nox are required on the local system e.g. archlinux.
• Many format checkers are pinned in .pre-commit-config.yaml.

Fix

• docs: pre-commit install instruction in readme.

Feat

• docs: pages.yml generates gh-pages.

Update

• build: manual update poetry deps
• build(deps): bump virtualenv in /.github/workflows (#53)
• build(deps): bump nox from 2022.8.7 to 2022.11.21 in /.github/workflows (#50)
• build(deps): bump numpy from 1.23.4 to 1.23.5 (#52)
• build(deps): bump pandas from 1.5.1 to 1.5.2 (#51)
• build(deps): bump rpy2 from 3.5.5 to 3.5.6 (#49)
• build(deps): bump pip from 22.3 to 22.3.1 in /.github/workflows (#47)

v0.3.11 (2022-11-04)

Fix

• docs build and update deps

Update

• build(deps): bump virtualenv in /.github/workflows (#43)
• build(deps): bump actions/setup-python from 1 to 4 (#42)

v0.3.10 (2022-11-02)

Feat

• Add --fit-all flag exporting fit along with data.
• Always export all available data (directory hard coded).

Refactor

• Avoid code introspection.
• Use fit_routine() in main.
• Add Metadata and PlateScheme dataclasses.
• Map and filter for metadata manipulation.
• TitrationAnalysis inherits from Titration.
• Class method moved out of class into module level function.
• tit and titan .data can be None -> many type ignore required.
• buffer_wells set to components.
• slots and InitVar for lines in Labelblock, but dataclass slots works only in py3.10.
• Labelblock is created by a list-of-lines.
• Considered: LabelblockList(OrderedList).

Update

• build(deps): bump seaborn from 0.12.0 to 0.12.1 (#29)
• build(deps): bump scipy from 1.9.1 to 1.9.3 (#28)
• build(deps): bump pandas from 1.5.0 to 1.5.1 (#27)
• build(deps): bump pip from 22.2.2 to 22.3 in /.github/workflows (#26)
• build(deps): bump pandas-stubs from 1.4.4.220919 to 1.5.0.221012 (#25)
• build(deps): bump numpy from 1.23.3 to 1.23.4 (#24)
• build(deps): bump rpy2 from 3.5.4 to 3.5.5 (#23)
• build(deps): bump poetry from 1.2.0 to 1.2.2 in /.github/workflows (#21)
• build(deps): bump emcee from 3.1.2 to 3.1.3 (#18)
• build(deps): bump codecov/codecov-action from 3.1.0 to 3.1.1 (#16)
• build(deps): bump actions/setup-python from 1 to 4 (#15)

v0.3.9 (2022-10-02)

Feat

• LabelblocksGroup metadata now list all values if not identical.
• [ci] Add nox -s bump.
• [ci] Add nox -s coverage and codecov flag in readme.

Refactor

• Removed temperatures attribute as already present in metadata.
• Slightly improved design for TecanfilesGroup(List[Tecanfile]).
• Prototyped NormalizedLabelblock class.
• Removed of os.path in favor of pathlib.Path

v0.3.8 (2022-09-24)

Fix

• missing xlrd issue.

v0.3.7 (2022-09-23)

Fix

• clop prtecan Install from pipx.

Refactor

• Path and str are mixing.
• tests do not use os.chdir() anymore.

v0.3.6 (2022-09-21)

Feat

• [docs] Add click-sphinx.

Fix

• pipx installation?
• Remain an issue in lbG test ph5,cl20 all metadata are list (exception str).

Refactor

• dataclasses in prtecan.
• string normalization to black default.
• [ci] isort and pyupgrade from pre-commit.
• [ci] safety.
• [docs] README.md and CHANGELOG.md.

v0.3.5 (2022-09-11)

Changed

• Update poetry 1.2.0 and notebook.

v0.3.4 (2022-09-07)

Fixed

• Python deps ">3.8, <3.11" in pyproject.

Changed

• Update poetry 1.2.0 and notebook.

v0.3.3 (2022-05-27)

• Update deps for notebooks.

v0.3.2 (2022-03-15)

• Add zenodo.

v0.3.1 (2022-03-14)

Fixed

• Removed :math: directive from README.rst and plantuml.

v0.3.0 (2022-03-14)

Fixed

• warning for keys_unk set used as index in pd.

Added

• Tecan file parser.
• Import fit_titrations scripts with many test data.
• usage.org (exported to .rst) serves as tutorial in docs and includes:
  • liaisan-data
  • new-bootstrap
  • lmfit global
  • emcee (extremely slow)
• command clop.
• (docs) usage.org.
• Adopt pre-commit, poetry and nox.
• https://pypi.org/project/readme-renderer/ in lint.
• (build) Github actions.

Changed

• Update to python 3.9 and 3.10.

• Update dependencies:

  poetry show --outdated
  

  with required minor changes in old scripts.

• nox-poetry.

• pandas.rpy (<=0.19) now lives in rpy2.

v0.2.1 (2021-11-18)

• Update to python 3.6.
• Py.test for:
  • fit_titration.py
  • fit_titration_global.py
• lmfit==0.8.3 to prevent fit-titration_global.py to fail.
• [_tmpoutput]{.title-ref} is not deleted; watch out for false positive.

v0.2.0 (2021-11-14)

• Reference for running older scripts; reproducibility thanks to Poetry and Pyenv:

  LDFLAGS=-L/usr/lib/openssl-1.0/ CFLAGS=-I/usr/include/openssl-1.0/ \
    pyenv install 3.4.10
  ++CONFIGURE_OPTS="--without-ensurepip" pyenv install 3.5.8++
  CC=clang pyenv install 3.5.10
  poetry env use 3.5
  poetry install
  .. fit_titration.py Meas/A04\ Cl_A.csv NTT-A04-Cl_note -t cl -d output-enspire
  .. fit_titration_global.py D05.dat output-D05 --boot 99
  .. fit_titration_global.py -t cl --boot 999 B05-20130628-cor.dat output-B05
  

• Note that fit_rpy.py did never work (indeed did not use #!/usr/bin/env python).

• Tested dependencies for fit_titration (without warnings):

  cycler          0.10.0 Composable style cycles
  lmfit           0.8.3  Least-Squares Minimization with Bounds and Constraints
  matplotlib      1.5.3  Python plotting package
  numpy           1.10.4 NumPy: array processing for numbers, strings, …
  pandas          0.18.1 Powerful data structures for data analysis, …
  pyparsing       2.4.7  Python parsing module
  python-dateutil 2.8.1  Extensions to the standard Python datetime module
  pytz            2021.3 World timezone definitions, modern and historical
  rpy2            2.3.10 Python interface to the R language (embedded R)
  scipy           0.18.1 SciPy: Scientific Library for Python
  seaborn         0.7.1  Seaborn: statistical data visualization
  six             1.16.0 Python 2 and 3 compatibility utilities
  

0.1.0 (2021-3-4)

• Initial placeholder.