From de371d36840fa8a68d3a3a38bcd4de93c7042d8a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 13:22:19 +0000 Subject: [PATCH 1/7] chore: migrate from poetry to hatchling with dynamic versioning Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/f746f481-8c8f-4397-8c9e-f4609a354055 Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- pyproject.toml | 45 +++++++++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 20 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c4af95c..8ea8d5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,13 +1,13 @@ -[tool.poetry] +[project] name = "quantms-utils" +dynamic = ["version"] description = "Python scripts and helpers for the quantMS workflow" readme = "README.md" license = "MIT" -version = "0.0.27" authors = [ - "Yasset Perez-Riverol ", - "Dai Chengxin ", - "Julianus Pfeuffer " + { name = "Yasset Perez-Riverol", email = "ypriverol@gmail.com" }, + { name = "Dai Chengxin", email = "chengxin2024@126.com" }, + { name = "Julianus Pfeuffer", email = "jule.pf@gmail.com" } ] keywords = [ "quantms", @@ -24,26 +24,22 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", "Development Status :: 5 - Production/Stable" ] -packages = [ - { include = "quantmsutils" } +dependencies = [ + "click", + "sdrf-pipelines>=0.1.2", + "pyopenms>=3.3.0", + "pandas", + "pyarrow>=16.1.0", + "scipy", ] -[tool.poetry.dependencies] -python = "*" -click = "*" -sdrf-pipelines = ">=0.1.2" -pyopenms = ">=3.3.0" -pandas = "*" -pyarrow = ">=16.1.0" -scipy = "*" - -[tool.poetry.urls] +[project.urls] GitHub = "https://github.com/bigbio/quantms-utils" PyPi = "https://pypi.org/project/quantms-utils/" Quantms = "https://quantms.org" LICENSE = "https://github.com/bigbio/quantms-utils/blob/main/LICENSE" -[tool.poetry.scripts] +[project.scripts] quantmsutilsc = "quantmsutils.quantmsutilsc:main" [tool.isort] @@ -54,5 +50,14 @@ line-length = 99 target-version = ["py39"] [build-system] -requires = ["poetry-core>=1.2.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + +[tool.hatch.version] +source = "vcs" + +[tool.hatch.version.raw-options] +local_scheme = "no-local-version" + +[tool.hatch.build.targets.wheel] +packages = ["quantmsutils"] From ba602a52623b966c3d95eec0c180250181e58885 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Mon, 30 Mar 2026 16:05:27 +0200 Subject: [PATCH 2/7] Update meta.yaml --- recipe/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index b318cac..dcbbeb7 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -19,12 +19,11 @@ requirements: host: - python - pip - - poetry-core >=1.2.0 - + - hatchling run: - python >=3.9,<3.13 - click - - sdrf-pipelines >=0.1.1 + - sdrf-pipelines >=0.1.2 - pyopenms>=3.3.0 - pandas - pyarrow>=16.1.0 From 18804967d7af30fa9572734e055e29501fe9e1d4 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 14:14:26 +0000 Subject: [PATCH 3/7] fix: add hatch-vcs to conda recipe host requirements and update version Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/2a55fdd0-97c0-4013-89ff-d3d9718d9ea5 Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- recipe/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index dcbbeb7..ed4e9c2 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,7 +1,7 @@ # recipe/meta.yaml package: name: quantms-utils - version: "0.0.26" + version: "0.0.27" source: path: ../ @@ -20,6 +20,7 @@ requirements: - python - pip - hatchling + - hatch-vcs run: - python >=3.9,<3.13 - click From 6084f694c9709c3f2b3fd4ac85ee225ae978d8c4 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 15:00:12 +0000 Subject: [PATCH 4/7] chore: remove .DS_Store files and add to .gitignore Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/49b172a3-51a0-40db-890c-f426fb347061 Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- .DS_Store | Bin 8196 -> 0 bytes .gitignore | 3 +++ quantmsutils/.DS_Store | Bin 6148 -> 0 bytes tests/.DS_Store | Bin 8196 -> 0 bytes 4 files changed, 3 insertions(+) delete mode 100644 .DS_Store delete mode 100644 quantmsutils/.DS_Store delete mode 100644 tests/.DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index ccbc9c30933b1a5d8e3a4d771d0ebfad6fa5c15a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8196 zcmeHM&x_MQ6n@j6DXUmSVOb~yyveGqT?>ns*sbEhlM#PQH)%^7Oq1B87A?i%$pt<6 zFBJ5k;K7TYyr`fk9>o8^KSS_MX1blU+p-s3!Fe$AP3OIr_w{SY?8^cGDR=7yfMozs za8S%H;k1KMKOHj`<2x&e1oOde7WA6i_GTjGhEzZ*AQg}bNCl(<|B3>5W>Zt8_XHe=CRh-N{d?;3HBIJE)@p4svhfH|Qc-V1plF9~%`H#fsdGpHH9j-+At}MYVSmAK@K; zMR}*7gNoOXt2eE5{Moc$H+#Ov@AkK*XIp-d z&;KB?cp{lfD`{m(xuv(@+AuF$jb1f-Xv1{^!*Uv(Fu|%f zFy!VH%c;A)vfFj)eweE>hmuh;)$B^Yf2^=}GQX-8OQpf8+Fz&ZwPI;7$S8-8oH%{4 zdfRS0?qez*9(DXk#5*!-Pw=DgorJr9EyQj$^w{6L*O`|EW0Aqyl@WK%CWHrv3lf`S1VtkfAIs6_5)2X$454qF2gTW&DT4 zbV1r{t2j1sP@{1}hG7a$G=%Pl?KtB0KMZlLa-YU=$Phhf@gPf!Se^r6scDNdU diff --git a/.gitignore b/.gitignore index 1f0d4d6..7def66f 100644 --- a/.gitignore +++ b/.gitignore @@ -169,6 +169,9 @@ cython_debug/ .qodo /tests/test_data/RD139_Narrow_UPS1_0_1fmol_inj1.mzML +# macOS metadata files +.DS_Store + # DIA-NN config file generated by tests diann_config.cfg diff --git a/quantmsutils/.DS_Store b/quantmsutils/.DS_Store deleted file mode 100644 index ed96f8a40116e5fd93d9ca99b532992aefb3211b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKJ5Iwu5S>k27|}#XAS8rj8v3+UCNdojvgjd%KoQFkAq}GNB{&9Gprqm=TmtcC zXKN=ypJPsUbWO9# zO+RmC+rV#BKpucG?%E~YQ{(?~eyBXL22NZBZ`xL-7D_m!>qMBEYJVCg;cY)0=YE(FJ2W z8sLk-Ho}`T4lvfSCgNXTL1t6 diff --git a/tests/.DS_Store b/tests/.DS_Store deleted file mode 100644 index f0f652ed9d707684cbb3e00d30d5363678af9c5e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8196 zcmeHMU2GIp6h3FVz`cQ%X)Qy6E^I6a) zO-&Pjh^WN)^WcLfYUIHfqKPI%(Zs|DHIWA;2vMVnPbMZN8jTM|J$LRbp{2YK<4>5I z+){zu*D7vqfRoxcB93)J7hNJa9vLKztt(RE121a!ShJ(?Ly; z0+19bKv1Ypc|d?kgfbP%DJcUettqny451jN7%1U1pAhCGQ=y!aQo;cx958$`h8YS5 zPbXX=Fb7OY8MToIA`e{c0TDi&GIkR@YOl!Oz45H=W@+|JcHFi+zp3d0DiyIgbLX*n zY(6`X9(7A;U-t`Mhn^o1TA%CM*>Ydc4p?R>qt*FP|rQPqNH?lo=Qw~A($?wejlUFgvvdvdO` zCvO(%aDzG5E{r)eQ=QZ8T!D+?S{=;+q-w(bH1`_p~`D`?O@UJtgLPJmn_2{-KTpw(=jaP z@G$wz@vTFandjAbmiIaOm>Hn7#o7|4Hn5>W);e0S{QKov_1bc-zRmUhZoK^a3Sx9beB>gZJBd*0kl&Cf>}{ zU3{=8PbLRjcq^;MBp=GTV`H>$PY$PKwY8`bk> zZ;3c0F`ZfuW5N5NaRJ(9SiT!h)@!>N+b5Q5Hw;=yty);wyGPULm0C{GBF2)lC2`fy z7-J2oMoFB&eGRE5snyP4lenLjKoZ)Z8-^hV4wT>tcoI&+3vdcf!&~q^d<>t!r*IBF zhp*sk_y)d(@8Ku-8GeCZu>u!hC05~5Y`~Rx3$Df_-hs`y1zWHUx8n}niM#M#9L5nm zfCupqx;Ty=`Z$S?;&FToPvGDkCG&Pmbjvq`5V9 znM#s;Wxid>>4c-J#Ir!B5qvUC}b_Y=3xV>6?z9EIvU!D4n^Sg%O%xH^Z} zFV&T+NS#Z}m+GyJ@wlo`z)AJ?b#bm%P&n}byRnf}43*7WI9Fp7SaNRbU8I7DX{on& z&`Kgq{sy|f1h2sxa0Wgkx?X@UiKIWmZ}11kh@2YM;WDhpI1zLWHsWmoNjDQk@5EN@ z!fv8z4-qwu{Wyq2xDT^vpc#<$Xh7BiK8REJ5I&5L;7NQ6pT=kKS$qy(B;vk4gOWR^ zQxe~sosz|L-mzWhFwK_9JRKNm*Xe-@iK`R&|F&!Y{(qgTN3h5Pkq7<{9>7>vx~qeB zdaduP$h8wx@1rV;u$z)HfKU^p<0ON0oaE(y7*an$rUH`+<&=~(LggR-Awc};8r}cV L{U5OJ#%=xrG&&L| From 63970115132e5eadaa635d712561ea21934a20a3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 15:10:31 +0000 Subject: [PATCH 5/7] chore: remove recipe/meta.yaml and conda-build CI/CD workflow Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/de4368e4-321e-4716-949a-b7ce00f4fc5c Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- .github/workflows/conda-build.yml | 34 ---------------------- recipe/conda_build_config.yaml | 2 -- recipe/meta.yaml | 47 ------------------------------- 3 files changed, 83 deletions(-) delete mode 100644 .github/workflows/conda-build.yml delete mode 100644 recipe/conda_build_config.yaml delete mode 100644 recipe/meta.yaml diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml deleted file mode 100644 index 34dbabb..0000000 --- a/.github/workflows/conda-build.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Conda Build - -on: [push, pull_request] - -jobs: - build: - runs-on: ubuntu-latest - defaults: - run: - shell: bash -el {0} - steps: - - name: Checkout repository - uses: actions/checkout@v4 # Update to latest version - - - name: Set up Miniconda - uses: conda-incubator/setup-miniconda@v3 - with: - mamba-version: "*" - channels: conda-forge,bioconda - cache-downloads: true - auto-update-conda: false - activate-environment: test - python-version: "3.12" - - - name: Setup conda-build and anaconda-client - run: | - mamba install -q conda-build anaconda-client conda-verify - - - name: Build package - run: | - conda build purge-all - conda config --set solver libmamba - conda config --set channel_priority strict - conda build recipe --suppress-variables --override-channels --channel conda-forge --channel bioconda --no-anaconda-upload --output-folder ./ \ No newline at end of file diff --git a/recipe/conda_build_config.yaml b/recipe/conda_build_config.yaml deleted file mode 100644 index 81e2ea5..0000000 --- a/recipe/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -python: - - 3.11 diff --git a/recipe/meta.yaml b/recipe/meta.yaml deleted file mode 100644 index ed4e9c2..0000000 --- a/recipe/meta.yaml +++ /dev/null @@ -1,47 +0,0 @@ -# recipe/meta.yaml -package: - name: quantms-utils - version: "0.0.27" - -source: - path: ../ - -build: - entry_points: - - quantmsutilsc=quantmsutils.quantmsutilsc:main - run_exports: - - {{ pin_subpackage('quantms-utils', max_pin="x.x") }} - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" - number: 0 - noarch: python - -requirements: - host: - - python - - pip - - hatchling - - hatch-vcs - run: - - python >=3.9,<3.13 - - click - - sdrf-pipelines >=0.1.2 - - pyopenms>=3.3.0 - - pandas - - pyarrow>=16.1.0 - - scipy -test: - imports: - - quantmsutils - commands: - - quantmsutilsc --help - -about: - home: https://www.github.com/bigbio/quantms-utils - summary: Python package with scripts and helpers for the quantms workflow - license: MIT - license_file: LICENSE - dev_url: https://www.github.com/bigbio/quantms-utils - -extra: - recipe-maintainers: - - ypriverol From 29bce255334de00883ba2e6e5fc4658b42f93c84 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 15:23:01 +0000 Subject: [PATCH 6/7] ci: replace poetry build with python -m build in workflow Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/c1761e1e-b832-4f20-8b19-1b96882d1458 Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- .github/workflows/python-package.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index aeee5d8..d225324 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -27,10 +27,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest + python -m pip install flake8 pytest build if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install poetry - poetry build + python -m build pip install dist/*.whl - name: Lint with flake8 run: | From df7a417f278db4635ede3f0649c0da4e3d095602 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 30 Mar 2026 15:28:53 +0000 Subject: [PATCH 7/7] ci: fix python-app.yml to use python -m build instead of poetry Agent-Logs-Url: https://github.com/bigbio/quantms-utils/sessions/56c363e3-440c-4fa7-904b-542e16a3864d Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com> --- .github/workflows/python-app.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index e6975c0..417b96b 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -26,10 +26,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install flake8 pytest + python -m pip install flake8 pytest build if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install poetry - poetry build + python -m build pip install dist/*.whl - name: Lint with flake8 run: | @@ -39,4 +38,4 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - poetry run pytest \ No newline at end of file + pytest \ No newline at end of file