From c675d1e90e859c9d042ea38ae1502a3e532feab1 Mon Sep 17 00:00:00 2001 From: Ludwig Lautenbacher Date: Fri, 15 Dec 2023 18:27:17 +0100 Subject: [PATCH 1/6] Read instrument_type from mzml --- spectrum_fundamentals/constants.py | 1 + 1 file changed, 1 insertion(+) diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index cd8644c..ce4115c 100644 --- a/spectrum_fundamentals/constants.py +++ b/spectrum_fundamentals/constants.py @@ -244,6 +244,7 @@ "MASS_ANALYZER", "FRAGMENTATION", "COLLISION_ENERGY", + "INSTRUMENT_TYPES" ] MZML_DATA_COLUMNS = SHARED_DATA_COLUMNS + MZML_ONLY_DATA_COLUMNS From ae6616f304d8d20af8fd5e134a2d77b557667340 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 18 Dec 2023 16:11:02 +0100 Subject: [PATCH 2/6] fixed pre-commit hooks --- spectrum_fundamentals/constants.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index ce4115c..f612eef 100644 --- a/spectrum_fundamentals/constants.py +++ b/spectrum_fundamentals/constants.py @@ -244,7 +244,7 @@ "MASS_ANALYZER", "FRAGMENTATION", "COLLISION_ENERGY", - "INSTRUMENT_TYPES" + "INSTRUMENT_TYPES", ] MZML_DATA_COLUMNS = SHARED_DATA_COLUMNS + MZML_ONLY_DATA_COLUMNS From fa5212594b3e56ec715defdc00ce5e0d07d66ed0 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 18 Dec 2023 16:12:45 +0100 Subject: [PATCH 3/6] Bump version from 0.4.4 to 0.4.5 --- .cookietemple.yml | 2 +- .github/release-drafter.yml | 4 ++-- cookietemple.cfg | 2 +- docs/conf.py | 4 ++-- pyproject.toml | 2 +- spectrum_fundamentals/__init__.py | 2 +- spectrum_fundamentals/__main__.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.cookietemple.yml b/.cookietemple.yml index d486c86..28b13ac 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Victor Giurcoiu email: victor.giurcoiu@tum.de project_name: spectrum_fundamentals project_short_description: Fundamentals public repo -version: 0.4.4 +version: 0.4.5 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index bbbbd74..cddc790 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.4.4 🌈" # <> -tag-template: 0.4.4 # <> +name-template: "0.4.5 🌈" # <> +tag-template: 0.4.5 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index 1af0672..ed112a0 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.4.4 +current_version = 0.4.5 [bumpversion_files_whitelisted] init_file = spectrum_fundamentals/__init__.py diff --git a/docs/conf.py b/docs/conf.py index aed7999..4d95802 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -54,9 +54,9 @@ # the built documents. # # The short X.Y version. -version = "0.4.4" +version = "0.4.5" # The full version, including alpha/beta/rc tags. -release = "0.4.4" +release = "0.4.5" # 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 1c2419b..0b3ef22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_fundamentals" -version = "0.4.4" # <> +version = "0.4.5" # <> description = "Fundamentals public repo" authors = ["WassimG "] license = "MIT" diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py index e529573..baef6e6 100644 --- a/spectrum_fundamentals/__init__.py +++ b/spectrum_fundamentals/__init__.py @@ -1,7 +1,7 @@ """Initialize fundamentals.""" __author__ = "Victor Giurcoiu" __email__ = "victor.giurcoiu@tum.de" -__version__ = "0.4.4" +__version__ = "0.4.5" import logging import logging.handlers diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py index e816ca5..1f59788 100644 --- a/spectrum_fundamentals/__main__.py +++ b/spectrum_fundamentals/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.4.4", message=click.style("spectrum_fundamentals Version: 0.4.4")) +@click.version_option(version="0.4.5", message=click.style("spectrum_fundamentals Version: 0.4.5")) def main() -> None: """spectrum_fundamentals.""" From e8d65cf8b5b7f31fe06e84ff29dc053c48006f95 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 18 Dec 2023 17:59:22 +0100 Subject: [PATCH 4/6] Bump version from 0.4.5 to 0.5.0 --- .cookietemple.yml | 2 +- .github/release-drafter.yml | 4 ++-- cookietemple.cfg | 2 +- docs/conf.py | 4 ++-- pyproject.toml | 2 +- spectrum_fundamentals/__init__.py | 2 +- spectrum_fundamentals/__main__.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.cookietemple.yml b/.cookietemple.yml index 28b13ac..c04f2ec 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Victor Giurcoiu email: victor.giurcoiu@tum.de project_name: spectrum_fundamentals project_short_description: Fundamentals public repo -version: 0.4.5 +version: 0.5.0 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index cddc790..2696532 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.4.5 🌈" # <> -tag-template: 0.4.5 # <> +name-template: "0.5.0 🌈" # <> +tag-template: 0.5.0 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index ed112a0..5782fc6 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.4.5 +current_version = 0.5.0 [bumpversion_files_whitelisted] init_file = spectrum_fundamentals/__init__.py diff --git a/docs/conf.py b/docs/conf.py index 4d95802..05272d7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -54,9 +54,9 @@ # the built documents. # # The short X.Y version. -version = "0.4.5" +version = "0.5.0" # The full version, including alpha/beta/rc tags. -release = "0.4.5" +release = "0.5.0" # 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 0b3ef22..dcce2bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_fundamentals" -version = "0.4.5" # <> +version = "0.5.0" # <> description = "Fundamentals public repo" authors = ["WassimG "] license = "MIT" diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py index baef6e6..20ea424 100644 --- a/spectrum_fundamentals/__init__.py +++ b/spectrum_fundamentals/__init__.py @@ -1,7 +1,7 @@ """Initialize fundamentals.""" __author__ = "Victor Giurcoiu" __email__ = "victor.giurcoiu@tum.de" -__version__ = "0.4.5" +__version__ = "0.5.0" import logging import logging.handlers diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py index 1f59788..4f2b12a 100644 --- a/spectrum_fundamentals/__main__.py +++ b/spectrum_fundamentals/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.4.5", message=click.style("spectrum_fundamentals Version: 0.4.5")) +@click.version_option(version="0.5.0", message=click.style("spectrum_fundamentals Version: 0.5.0")) def main() -> None: """spectrum_fundamentals.""" From 4d9fd43a39eb5b1489828a93251365c7a4aeb1bd Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 18 Dec 2023 18:13:34 +0100 Subject: [PATCH 5/6] corrected author to M.Picciani --- spectrum_fundamentals/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py index 20ea424..8e7d2f1 100644 --- a/spectrum_fundamentals/__init__.py +++ b/spectrum_fundamentals/__init__.py @@ -1,6 +1,6 @@ """Initialize fundamentals.""" -__author__ = "Victor Giurcoiu" -__email__ = "victor.giurcoiu@tum.de" +__author__ = "Mario Picciani" +__email__ = "mario.picciani@tum.de" __version__ = "0.5.0" import logging From 2e9ad759172977effed21d542e4adf71b8e0d2e7 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 18 Dec 2023 18:22:36 +0100 Subject: [PATCH 6/6] updated authors and actors --- .github/workflows/sync_project.yml | 6 +++--- LICENSE | 2 +- pyproject.toml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml index a5420b2..7d1d68b 100644 --- a/.github/workflows/sync_project.yml +++ b/.github/workflows/sync_project.yml @@ -25,9 +25,9 @@ jobs: - uses: oleksiyrudenko/gha-git-credentials@v2.1 with: - name: "victorgiurcoiu" - email: "victor.giurcoiu@tum.de" - actor: "victorgiurcoiu" + name: "Mario Picciani" + email: "mario.picciani@tum.de" + actor: "picciama" token: "${{ secrets.CT_SYNC_TOKEN}}" - name: Sync project diff --git a/LICENSE b/LICENSE index 0174082..ad0a6b1 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022, Victor Giurcoiu +Copyright (c) 2023, Wilhelmlab at Technical University of Munich Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/pyproject.toml b/pyproject.toml index dcce2bc..dba24c6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,8 @@ [tool.poetry] name = "spectrum_fundamentals" version = "0.5.0" # <> -description = "Fundamentals public repo" -authors = ["WassimG "] +description = "Fundamental functions, annotation pipeline and constants for oktoberfest" +authors = ["Wilhelmlab at Technical University of Munich"] license = "MIT" readme = "README.rst" homepage = "https://github.com/wilhelm-lab/spectrum_fundamentals"