From 20b7a16c193976753d1e9b05e1214b8acc0b879d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:08:10 +0000 Subject: [PATCH 01/11] [DEPENDABOT]: Bump peaceiris/actions-gh-pages from 3 to 4 Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) --- updated-dependencies: - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/publish_docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 025589b..11d3f2e 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -30,7 +30,7 @@ jobs: - name: Deploy if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}} - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./docs/_build/html From 23ce568187c21ab8c620ed460722598dc8adfb3f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Apr 2024 10:08:13 +0000 Subject: [PATCH 02/11] [DEPENDABOT]: Bump release-drafter/release-drafter from 5 to 6 Bumps [release-drafter/release-drafter](https://github.com/release-drafter/release-drafter) from 5 to 6. - [Release notes](https://github.com/release-drafter/release-drafter/releases) - [Commits](https://github.com/release-drafter/release-drafter/compare/v5...v6) --- updated-dependencies: - dependency-name: release-drafter/release-drafter dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/release_drafter.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release_drafter.yml b/.github/workflows/release_drafter.yml index 41f8209..46853d2 100644 --- a/.github/workflows/release_drafter.yml +++ b/.github/workflows/release_drafter.yml @@ -14,6 +14,6 @@ jobs: update_release_draft: runs-on: ubuntu-latest steps: - - uses: release-drafter/release-drafter@v5 + - uses: release-drafter/release-drafter@v6 env: GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}" From 6e6b5400ef0b081e63a8ba7d144acee8aa22847a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 May 2024 10:23:07 +0000 Subject: [PATCH 03/11] [DEPENDABOT]: Bump lxml from 4.9.4 to 5.2.2 Bumps [lxml](https://github.com/lxml/lxml) from 4.9.4 to 5.2.2. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](https://github.com/lxml/lxml/compare/lxml-4.9.4...lxml-5.2.2) --- updated-dependencies: - dependency-name: lxml dependency-type: direct:production update-type: version-update:semver-major ... 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htmlsoup = ["BeautifulSoup4"] -source = ["Cython (==0.29.37)"] +source = ["Cython (>=3.0.10)"] [[package]] name = "markdown-it-py" @@ -3270,4 +3316,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11.0" -content-hash = "8b8fff799603c037760578a6d90143064efc9d63d429f7f322d850525439a558" +content-hash = "067c3bb6ecad61000fcd7838724860ad32235925e3a8c3e09e09d4312a516dbb" diff --git a/pyproject.toml b/pyproject.toml index 0651f6e..5848366 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ pandas = "^1.3.0" h5py = "^3.1.0" pymzml = "^2.5.0" pyteomics = "^4.3.3" -lxml= '^4.5.2' +lxml= '>=4.5.2,<6.0.0' spectrum-fundamentals = ">=0.5.2,<0.6.0" alphatims = "^1.0.8" sortedcontainers = "^2.4.0" From 74b4a15794173ae2c0f8e39ecd2c98c2aff997ba Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 May 2024 10:15:36 +0000 Subject: [PATCH 04/11] [DEPENDABOT]: Bump pytest from 8.1.2 to 8.2.1 Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.1.2 to 8.2.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/8.1.2...8.2.1) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index fb7b3e8..d1b3a4c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2112,13 +2112,13 @@ xml = ["lxml", "numpy"] [[package]] name = "pytest" -version = "8.1.2" +version = "8.2.1" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" files = [ - {file = "pytest-8.1.2-py3-none-any.whl", hash = "sha256:6c06dc309ff46a05721e6fd48e492a775ed8165d2ecdf57f156a80c7e95bb142"}, - {file = "pytest-8.1.2.tar.gz", hash = "sha256:f3c45d1d5eed96b01a2aea70dee6a4a366d51d38f9957768083e4fecfc77f3ef"}, + {file = "pytest-8.2.1-py3-none-any.whl", hash = "sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1"}, + {file = "pytest-8.2.1.tar.gz", hash = "sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd"}, ] [package.dependencies] @@ -2126,11 +2126,11 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" -pluggy = ">=1.4,<2.0" +pluggy = ">=1.5,<2.0" tomli = {version = ">=1", markers = "python_version < \"3.11\""} [package.extras] -testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] [[package]] name = "python-dateutil" From 3fe1f92a323cbb156813787f3089111162bd05d5 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sun, 26 May 2024 11:02:32 +0200 Subject: [PATCH 05/11] fix unknown mods not filtered out for sage --- spectrum_io/search_result/sage.py | 2 +- spectrum_io/search_result/search_results.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/spectrum_io/search_result/sage.py b/spectrum_io/search_result/sage.py index 5aa4caa..f03b504 100644 --- a/spectrum_io/search_result/sage.py +++ b/spectrum_io/search_result/sage.py @@ -58,7 +58,7 @@ def update_columns_for_prosit(df: pd.DataFrame, tmt_labeled: str) -> pd.DataFram ) # removing .mzML - df["RAW_FILE"] = df["RAW_FILE"].str.replace(".mzML", "", regex=True) + df["RAW_FILE"] = df["RAW_FILE"].str.replace(r"\.mz[M|m][l|L]", "", regex=True) # extracting only the scan number df["SCAN_NUMBER"] = [int(x.rsplit("=", 1)[-1]) for x in df["SCAN_NUMBER"]] # creating a column of decoys and targets diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index 2160873..8e9a6b5 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -22,7 +22,7 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: # retain only peptides that fall within [7, 30] length supported by Prosit df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)] # remove unsupported mods to exclude - unsupported_mods = [r"Acetyl \(Protein N\-term\)", "ac", r"\[[0-9]+\]"] + unsupported_mods = [r"Acetyl \(Protein N\-term\)", "ac", r"\[[0-9]+\]", r"\+"] exclude_mods_pattern = re.compile("|".join(unsupported_mods)) df = df[~df["MODIFIED_SEQUENCE"].str.contains(exclude_mods_pattern)] # remove non-canonical aas From ff37316338b264041ba01fcfe7ca778d7cee7a48 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sun, 26 May 2024 11:08:30 +0200 Subject: [PATCH 06/11] fix mod masses for unit test --- tests/unit_tests/data/sage_output.tsv | 12 ++++++------ tests/unit_tests/test_sage.py | 5 +++-- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/tests/unit_tests/data/sage_output.tsv b/tests/unit_tests/data/sage_output.tsv index 043e04d..0b1596e 100644 --- a/tests/unit_tests/data/sage_output.tsv +++ b/tests/unit_tests/data/sage_output.tsv @@ -1,17 +1,17 @@ peptide proteins num_proteins filename scannr rank label expmass calcmass charge peptide_len missed_cleavages isotope_error precursor_ppm fragment_ppm hyperscore delta_next delta_best rt aligned_rt predicted_rt delta_rt_model matched_peaks longest_b longest_y longest_y_pct matched_intensity_pct scored_candidates poisson sage_discriminant_score posterior_error spectrum_q peptide_q protein_q ms1_intensity ms2_intensity [+229.1629]-HLDGGAEQSLLFVAGM[+15.9949]R rev_sp|P26006-1|ITA3_HUMAN;rev_sp|P26006|ITA3_HUMAN 2 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=50989 1 -1 2199.172 2045.0568 2 17 0 0.0 72623.49 7.826053 18.084579770792818 0.20642824189008735 0.0 113.94822 0.9495685 0.0 0.9495685 4 2 1 0.05882353 1.318411 84602 -2.0562283019710534 -0.37137848 -0.35820845 0.30232558 0.5880901 0.5815684 926232.0 7361.109 [+229.1629]-GRFVEPLSNVQEEWNQK[+229.1629] rev_sp|Q9H1A3-2|METL9_HUMAN;rev_sp|Q9H1A3|METL9_HUMAN;rev_tr|H3BN86|H3BN86_HUMAN;rev_tr|Q8TD49|Q8TD49_HUMAN 4 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 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0.8501851 0.0 0.8501851 4 1 2 0.06666667 1.6194082 80638 -2.046675752396668 -0.3724502 -0.35820845 0.30232558 0.5880901 0.5815684 643726.75 8588.239 [+229.1629]-VNM[+15.9949]RTSSSIQNEDEATSMELIAPGP sp|Q9Y5Y9|SCNAA_HUMAN;tr|A0A2R8Y6J6|A0A2R8Y6J6_HUMAN;tr|A0A590UJM0|A0A590UJM0_HUMAN 3 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=45493 1 1 3074.5525 2921.3948 3 25 1 0.0 51087.08 5.391072 19.979716393086438 0.2293833747943026 0.0 102.12942 0.85107845 0.0 0.85107845 5 1 2 0.08 1.4697478 154744 -2.71207222963538 -0.3737817 -0.35820845 0.30232558 0.5880901 0.5815684 1085421.8 8865.469 [+229.1629]-VGEQEAPHEGGHPGSDSARASMADWLR sp|Q9H093|NUAK2_HUMAN 1 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=41946 1 1 3229.3804 3075.4417 3 27 1 0.0 48832.06 2.6081188 20.936078174830033 0.05364075290029291 0.0 93.63916 0.7803263 0.0 0.7803263 4 1 1 0.037037037 6.790568 109802 -2.034297610829216 -0.37500644 -0.35820845 0.30232558 0.5880901 0.5815684 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GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=37376 1 1 3897.3843 3593.885 3 29 1 0.0 81027.46 5.0039053 21.88178474607965 0.07848479239995854 0.0 83.277466 0.6939789 0.0 0.6939789 4 1 2 0.06896552 2.1495197 58331 -2.045800246831915 -0.37965888 -0.35820845 0.30232558 0.5880901 0.5815684 18796730.0 52520.473 +[+229.1629]-C[+57.0215]LIQM[+15.9949]GAAVEAK[+229.1629]AYNGNTALHVAASLQYR tr|H7C5S1|H7C5S1_HUMAN 1 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=37376 1 1 3897.3843 3593.885 3 29 1 0.0 81027.46 5.0039053 21.88178474607965 0.07848479239995854 0.0 83.277466 0.6939789 0.0 0.6939789 4 1 2 0.06896552 2.1495197 58331 -2.045800246831915 -0.37965888 -0.35820845 0.30232558 0.5880901 0.5815684 18796730.0 52520.473 [+229.1629]-M[+15.9949]EESLNIVK[+229.1629]YTAFLYNDQLIWSGLEQDDMR sp|P86790|CCZ1B_HUMAN;sp|P86791|CCZ1_HUMAN 2 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=41296 1 1 4398.7207 4095.037 3 30 1 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14758.541 [+229.1629]-EGRGAGSQSPPRGR sp|Q6ZSN1|YI023_HUMAN 1 GN20170722_SK_HLA_G0103_R1_01.mzML controllerType=0 controllerNumber=1 scan=45427 1 1 1942.9047 1639.8704 2 14 2 0.0 169161.78 4.145797 19.229664162247772 0.4602391019734071 0.0 101.96355 0.8496962 0.0 0.8496962 4 1 1 0.071428575 4.303446 136956 -2.026177700336816 -0.3904131 -0.35820845 0.30232558 0.5880901 0.5815684 993124.44 14842.607 diff --git a/tests/unit_tests/test_sage.py b/tests/unit_tests/test_sage.py index 40dcfb0..9faf7e7 100644 --- a/tests/unit_tests/test_sage.py +++ b/tests/unit_tests/test_sage.py @@ -12,7 +12,8 @@ class TestSage(unittest.TestCase): def test_read_sage(self): """Test function for reading sage results and transforming to Prosit format.""" expected_sage_internal_path = Path(__file__).parent / "data" / "sage_output_internal.csv" - internal_search_results_df = Sage(Path(__file__).parent / "data" / "sage_output.tsv").read_result() + internal_search_results_df = ( + Sage(Path(__file__).parent / "data" / "sage_output.tsv").read_result().reset_index(drop=True) + ) expected_df = pd.read_csv(expected_sage_internal_path) - pd.testing.assert_frame_equal(internal_search_results_df, expected_df) From 77aa3999884cc93511ead14068bc542d6f1ad40f Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sun, 26 May 2024 11:11:12 +0200 Subject: [PATCH 07/11] added TIMSTOF instrument type to output --- spectrum_io/d/bruker.py | 1 + 1 file changed, 1 insertion(+) diff --git a/spectrum_io/d/bruker.py b/spectrum_io/d/bruker.py index 60cc6b2..2f6da95 100644 --- a/spectrum_io/d/bruker.py +++ b/spectrum_io/d/bruker.py @@ -184,5 +184,6 @@ def read_and_aggregate_timstof(source: Path, tims_meta_file: Path) -> pd.DataFra df_combined["RAW_FILE"] = source.stem df_combined["MASS_ANALYZER"] = "TOF" df_combined["FRAGMENTATION"] = "HCD" + df_combined["INSTRUMENT_TYPES"] = "TIMSTOF" return df_combined From 5a9c28b73acae4a413c99dd413dc5dbdea394767 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sun, 26 May 2024 11:12:18 +0200 Subject: [PATCH 08/11] updated spectrum_fundamentals min dep --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0651f6e..72624b8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ h5py = "^3.1.0" pymzml = "^2.5.0" pyteomics = "^4.3.3" lxml= '^4.5.2' -spectrum-fundamentals = ">=0.5.2,<0.6.0" +spectrum-fundamentals = ">=0.5.4,<0.6.0" alphatims = "^1.0.8" sortedcontainers = "^2.4.0" From b02aaf781d89990f9316c740f74f62a202c6aafc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 May 2024 10:21:28 +0000 Subject: [PATCH 09/11] [DEPENDABOT]: Bump coverage from 7.5.0 to 7.5.2 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.5.0 to 7.5.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.5.0...7.5.2) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... 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Signed-off-by: dependabot[bot] --- .github/workflows/run_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 22612a0..d91eb1f 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -165,4 +165,4 @@ jobs: run: nox --force-color --session=coverage -- xml -i - name: Upload coverage report - uses: codecov/codecov-action@v3.1.1 + uses: codecov/codecov-action@v4.4.1 From 69897ce20eaa3ed76327603de9f22e70a8b0ceec Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Wed, 29 May 2024 13:48:51 +0200 Subject: [PATCH 11/11] Bump version from 0.4.3 to 0.4.4 --- .cookietemple.yml | 2 +- .github/release-drafter.yml | 4 ++-- cookietemple.cfg | 2 +- docs/conf.py | 4 ++-- pyproject.toml | 2 +- spectrum_io/__init__.py | 2 +- spectrum_io/__main__.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.cookietemple.yml b/.cookietemple.yml index ec9f43c..39b5c71 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Mario Picciani email: mario.picciani@tum.de project_name: spectrum_io project_short_description: IO related functionalities for oktoberfest. -version: 0.4.3 +version: 0.4.4 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index 91aa8c8..bbbbd74 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.4.3 🌈" # <> -tag-template: 0.4.3 # <> +name-template: "0.4.4 🌈" # <> +tag-template: 0.4.4 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index 1a0eb33..3ddd7be 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.4.3 +current_version = 0.4.4 [bumpversion_files_whitelisted] init_file = spectrum_io/__init__.py diff --git a/docs/conf.py b/docs/conf.py index a65f83a..e41df82 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -53,9 +53,9 @@ # the built documents. # # The short X.Y version. -version = "0.4.3" +version = "0.4.4" # The full version, including alpha/beta/rc tags. -release = "0.4.3" +release = "0.4.4" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pyproject.toml b/pyproject.toml index d6dd046..4ba27f5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_io" -version = "0.4.3" # <> +version = "0.4.4" # <> description = "IO related functionalities for oktoberfest." authors = ["Wilhelmlab at Technical University of Munich"] license = "MIT" diff --git a/spectrum_io/__init__.py b/spectrum_io/__init__.py index 5566d85..8130fd6 100644 --- a/spectrum_io/__init__.py +++ b/spectrum_io/__init__.py @@ -2,7 +2,7 @@ __author__ = "Mario Picciani" __email__ = "mario.picciani@tum.de" -__version__ = "0.4.3" +__version__ = "0.4.4" import logging import logging.handlers diff --git a/spectrum_io/__main__.py b/spectrum_io/__main__.py index 1e56b85..98dd70d 100644 --- a/spectrum_io/__main__.py +++ b/spectrum_io/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.4.3", message=click.style("spectrum_io Version: 0.4.3")) +@click.version_option(version="0.4.4", message=click.style("spectrum_io Version: 0.4.4")) def main() -> None: """spectrum_io."""