From 450f503b4cc1bb9b950ec3611910ed465bd3cf04 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 16:39:45 +0000 Subject: [PATCH 01/14] forcing more versions for compatibility. --- environment.yml | 1 + pyproject.toml | 3 ++- quantmsutils/__init__.py | 2 +- recipe/meta.yaml | 9 +++++---- requirements.txt | 2 ++ 5 files changed, 11 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 52e267b..1bea45a 100644 --- a/environment.yml +++ b/environment.yml @@ -14,3 +14,4 @@ dependencies: - ms2rescore=3.0.3 - deepLC=2.2.38 - psm-utils=0.8.3 + - scipy=1.13.1 diff --git a/pyproject.toml b/pyproject.toml index 858234f..0e8b493 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "quantms-utils" description = "Python scripts and helpers for the quantMS workflow" readme = "README.md" license = "MIT" -version = "0.0.14" +version = "0.0.15" authors = [ "Yasset Perez-Riverol ", "Dai Chengxin ", @@ -39,6 +39,7 @@ numpy = "*" pyarrow = "*" psm-utils = "0.8.3" deepLC = "2.2.38" +scipy = "1.13.1" [tool.poetry.urls] GitHub = "https://github.com/bigbio/quantms-utils" diff --git a/quantmsutils/__init__.py b/quantmsutils/__init__.py index 311f216..6561790 100644 --- a/quantmsutils/__init__.py +++ b/quantmsutils/__init__.py @@ -1 +1 @@ -__version__ = "0.0.14" +__version__ = "0.0.15" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 05dd300..79133f9 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,7 +1,7 @@ # recipe/meta.yaml package: name: quantms-utils - version: "0.0.14" + version: "0.0.15" source: path: ../ @@ -28,9 +28,10 @@ requirements: - pandas - numpy - pyarrow - - ms2rescore==3.0.3 - - deepLC==2.2.38 - - psm-utils=0.8.3 + - ms2rescore ==3.0.3 + - deepLC ==2.2.38 + - psm-utils ==0.8.3 + - scipy ==1.13.1 test: imports: - quantmsutils diff --git a/requirements.txt b/requirements.txt index eb5dbdf..2ad45e1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,3 +7,5 @@ numpy pyarrow deepLC==2.2.38 psm-utils==0.8.3 +scipy==1.13.1 + From 0c5d3c95a1d68fe06b4fb7e5eae350c3f6b2dbf9 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:16:01 +0000 Subject: [PATCH 02/14] forcing more versions --- environment.yml | 2 ++ pyproject.toml | 2 ++ recipe/meta.yaml | 2 ++ requirements.txt | 3 ++- 4 files changed, 8 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 1bea45a..1863ab0 100644 --- a/environment.yml +++ b/environment.yml @@ -15,3 +15,5 @@ dependencies: - deepLC=2.2.38 - psm-utils=0.8.3 - scipy=1.13.1 + - pygam=0.9.1 + - protobuf=3.19.6 diff --git a/pyproject.toml b/pyproject.toml index 0e8b493..6f12e7a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,8 @@ pyarrow = "*" psm-utils = "0.8.3" deepLC = "2.2.38" scipy = "1.13.1" +pygam = "0.9.1" +protobuf= "3.19.6" [tool.poetry.urls] GitHub = "https://github.com/bigbio/quantms-utils" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 79133f9..d9d7c7e 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -32,6 +32,8 @@ requirements: - deepLC ==2.2.38 - psm-utils ==0.8.3 - scipy ==1.13.1 + - pygam ==0.9.1 + - protobuf ==3.19.6 test: imports: - quantmsutils diff --git a/requirements.txt b/requirements.txt index 2ad45e1..b306c5a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,4 +8,5 @@ pyarrow deepLC==2.2.38 psm-utils==0.8.3 scipy==1.13.1 - +pygam==0.9.1 +protobuf==3.19.6 From 8c310f4a20a11e5dc268d13589cc922051c20c33 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:19:40 +0000 Subject: [PATCH 03/14] forcing more versions --- environment.yml | 2 +- pyproject.toml | 2 +- recipe/meta.yaml | 2 +- requirements.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 1863ab0..2be95d8 100644 --- a/environment.yml +++ b/environment.yml @@ -15,5 +15,5 @@ dependencies: - deepLC=2.2.38 - psm-utils=0.8.3 - scipy=1.13.1 - - pygam=0.9.1 + - pygam - protobuf=3.19.6 diff --git a/pyproject.toml b/pyproject.toml index 6f12e7a..1308dce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ pyarrow = "*" psm-utils = "0.8.3" deepLC = "2.2.38" scipy = "1.13.1" -pygam = "0.9.1" +pygam = "*" protobuf= "3.19.6" [tool.poetry.urls] diff --git a/recipe/meta.yaml b/recipe/meta.yaml index d9d7c7e..17f54b4 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -32,7 +32,7 @@ requirements: - deepLC ==2.2.38 - psm-utils ==0.8.3 - scipy ==1.13.1 - - pygam ==0.9.1 + - pygam - protobuf ==3.19.6 test: imports: diff --git a/requirements.txt b/requirements.txt index b306c5a..04842fe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,5 +8,5 @@ pyarrow deepLC==2.2.38 psm-utils==0.8.3 scipy==1.13.1 -pygam==0.9.1 +pygam protobuf==3.19.6 From 2a2d10301d5a79e7677bb2b833278a0e4bebf51e Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 16:39:45 +0000 Subject: [PATCH 04/14] forcing more versions for compatibility. --- environment.yml | 3 +++ pyproject.toml | 5 ++++- quantmsutils/__init__.py | 2 +- recipe/meta.yaml | 11 +++++++---- requirements.txt | 3 +++ 5 files changed, 18 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 52e267b..2be95d8 100644 --- a/environment.yml +++ b/environment.yml @@ -14,3 +14,6 @@ dependencies: - ms2rescore=3.0.3 - deepLC=2.2.38 - psm-utils=0.8.3 + - scipy=1.13.1 + - pygam + - protobuf=3.19.6 diff --git a/pyproject.toml b/pyproject.toml index 858234f..1308dce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "quantms-utils" description = "Python scripts and helpers for the quantMS workflow" readme = "README.md" license = "MIT" -version = "0.0.14" +version = "0.0.15" authors = [ "Yasset Perez-Riverol ", "Dai Chengxin ", @@ -39,6 +39,9 @@ numpy = "*" pyarrow = "*" psm-utils = "0.8.3" deepLC = "2.2.38" +scipy = "1.13.1" +pygam = "*" +protobuf= "3.19.6" [tool.poetry.urls] GitHub = "https://github.com/bigbio/quantms-utils" diff --git a/quantmsutils/__init__.py b/quantmsutils/__init__.py index 311f216..6561790 100644 --- a/quantmsutils/__init__.py +++ b/quantmsutils/__init__.py @@ -1 +1 @@ -__version__ = "0.0.14" +__version__ = "0.0.15" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 05dd300..17f54b4 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,7 +1,7 @@ # recipe/meta.yaml package: name: quantms-utils - version: "0.0.14" + version: "0.0.15" source: path: ../ @@ -28,9 +28,12 @@ requirements: - pandas - numpy - pyarrow - - ms2rescore==3.0.3 - - deepLC==2.2.38 - - psm-utils=0.8.3 + - ms2rescore ==3.0.3 + - deepLC ==2.2.38 + - psm-utils ==0.8.3 + - scipy ==1.13.1 + - pygam + - protobuf ==3.19.6 test: imports: - quantmsutils diff --git a/requirements.txt b/requirements.txt index eb5dbdf..04842fe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,3 +7,6 @@ numpy pyarrow deepLC==2.2.38 psm-utils==0.8.3 +scipy==1.13.1 +pygam +protobuf==3.19.6 From 640af8f18448ababadfe39912462a3cc6e4d306e Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:34:38 +0000 Subject: [PATCH 05/14] forcing more versions --- environment.yml | 2 +- pyproject.toml | 2 +- recipe/meta.yaml | 2 +- requirements.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 2be95d8..811067c 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ channels: dependencies: - click - sdrf-pipelines>=0.0.31 - - pyopenms + - pyopenms >=2.9.1 - pandas - numpy - pyarrow diff --git a/pyproject.toml b/pyproject.toml index 1308dce..5ca17cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ packages = [ python = ">=3.8,<3.12" click = "*" sdrf-pipelines = ">=0.0.31" -pyopenms = "*" +pyopenms = ">=2.9.1" ms2rescore = "3.0.3" pandas = "*" numpy = "*" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 17f54b4..f7dc57b 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -24,7 +24,7 @@ requirements: - python - click - sdrf-pipelines>=0.0.31 - - pyopenms + - pyopenms >=2.9.1 - pandas - numpy - pyarrow diff --git a/requirements.txt b/requirements.txt index 04842fe..3405caa 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ click sdrf-pipelines>=0.0.31 -pyopenms +pyopenms >=2.9.1 ms2rescore==3.0.3 pandas numpy From 55996ba1dec0d6ad0c3d8845b9d75477304eac07 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:49:16 +0000 Subject: [PATCH 06/14] forcing more versions --- .github/workflows/python-package.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3c47ffa..184778b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10"] steps: - uses: actions/checkout@v4 diff --git a/pyproject.toml b/pyproject.toml index 5ca17cb..0530120 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ packages = [ ] [tool.poetry.dependencies] -python = ">=3.8,<3.12" +python = ">=3.8,<3.11" click = "*" sdrf-pipelines = ">=0.0.31" pyopenms = ">=2.9.1" From a566ba3279d96bf261cac41203c2ca2012bf5609 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:51:35 +0000 Subject: [PATCH 07/14] forcing more versions --- environment.yml | 2 +- pyproject.toml | 2 +- recipe/meta.yaml | 2 +- requirements.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 811067c..2be95d8 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ channels: dependencies: - click - sdrf-pipelines>=0.0.31 - - pyopenms >=2.9.1 + - pyopenms - pandas - numpy - pyarrow diff --git a/pyproject.toml b/pyproject.toml index 0530120..ca5d136 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ packages = [ python = ">=3.8,<3.11" click = "*" sdrf-pipelines = ">=0.0.31" -pyopenms = ">=2.9.1" +pyopenms = "*" ms2rescore = "3.0.3" pandas = "*" numpy = "*" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index f7dc57b..17f54b4 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -24,7 +24,7 @@ requirements: - python - click - sdrf-pipelines>=0.0.31 - - pyopenms >=2.9.1 + - pyopenms - pandas - numpy - pyarrow diff --git a/requirements.txt b/requirements.txt index 3405caa..04842fe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ click sdrf-pipelines>=0.0.31 -pyopenms >=2.9.1 +pyopenms ms2rescore==3.0.3 pandas numpy From f81d8eaa9c9e27831f6fe22f3e58bf4d671bcf61 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:58:13 +0000 Subject: [PATCH 08/14] forcing more versions --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 184778b..3c47ffa 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v4 From 7291474089899cb72ae7995f0b86c2cdfb464abc Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 20:05:12 +0000 Subject: [PATCH 09/14] forcing more versions --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3c47ffa..2249c2d 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10"] steps: - uses: actions/checkout@v4 From 3b95be69afb3863714daf01544e18d724dab17fe Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 20:11:03 +0000 Subject: [PATCH 10/14] forcing more versions --- .github/workflows/conda-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml index 55ba3b2..72f49c6 100644 --- a/.github/workflows/conda-build.yml +++ b/.github/workflows/conda-build.yml @@ -20,7 +20,7 @@ jobs: cache-downloads: true auto-update-conda: false activate-environment: test - python-version: 3.11 + python-version: 3.10 - name: Setup conda-build and anaconda-client run: | From 3222ec8f3fca754f5ca9fd696aebaf9859b85905 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 20:16:33 +0000 Subject: [PATCH 11/14] forcing more versions --- .github/workflows/conda-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml index 72f49c6..43645c6 100644 --- a/.github/workflows/conda-build.yml +++ b/.github/workflows/conda-build.yml @@ -20,7 +20,7 @@ jobs: cache-downloads: true auto-update-conda: false activate-environment: test - python-version: 3.10 + python-version: "3.10" - name: Setup conda-build and anaconda-client run: | From be309a4d5b33af6fd961ccb16b507d86afb97095 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sat, 23 Nov 2024 07:40:25 +0000 Subject: [PATCH 12/14] forcing more versions --- recipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 17f54b4..d6d00c6 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -17,11 +17,11 @@ build: requirements: host: - - python + - python >=3.8 - pip - poetry-core >=1.2.0 run: - - python + - python >=3.7.0,<3.11 - click - sdrf-pipelines>=0.0.31 - pyopenms From 36dbf526a6fdb9dc035bb0c9c1f48987a3c9a364 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sat, 23 Nov 2024 09:36:18 +0000 Subject: [PATCH 13/14] forcing more versions --- recipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index d6d00c6..2b3fb7f 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -17,11 +17,11 @@ build: requirements: host: - - python >=3.8 + - python >=3.8,<3.11 - pip - poetry-core >=1.2.0 run: - - python >=3.7.0,<3.11 + - python >=3.8,<3.11 - click - sdrf-pipelines>=0.0.31 - pyopenms From 4fa3f129b75301b58ea118686cfe3c35b85637f4 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 22 Nov 2024 19:34:38 +0000 Subject: [PATCH 14/14] forcing more versions --- .github/workflows/conda-build.yml | 2 +- .github/workflows/python-package.yml | 2 +- pyproject.toml | 2 +- recipe/meta.yaml | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml index 55ba3b2..43645c6 100644 --- a/.github/workflows/conda-build.yml +++ b/.github/workflows/conda-build.yml @@ -20,7 +20,7 @@ jobs: cache-downloads: true auto-update-conda: false activate-environment: test - python-version: 3.11 + python-version: "3.10" - name: Setup conda-build and anaconda-client run: | diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3c47ffa..2249c2d 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10"] steps: - uses: actions/checkout@v4 diff --git a/pyproject.toml b/pyproject.toml index 1308dce..ca5d136 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ packages = [ ] [tool.poetry.dependencies] -python = ">=3.8,<3.12" +python = ">=3.8,<3.11" click = "*" sdrf-pipelines = ">=0.0.31" pyopenms = "*" diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 17f54b4..2b3fb7f 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -17,11 +17,11 @@ build: requirements: host: - - python + - python >=3.8,<3.11 - pip - poetry-core >=1.2.0 run: - - python + - python >=3.8,<3.11 - click - sdrf-pipelines>=0.0.31 - pyopenms