From a82291ea63ea84fc4a48e9b843b5451d19bf3241 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jul 2024 19:07:32 +0000 Subject: [PATCH 01/13] Update ms2rescore to 3.1.0 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 47c1ca6c892a4..68ff54cb4ee5e 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.0.3" %} +{% set version = "3.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: d2ecbe0dd3c23ce598265b265c83c84e515f50fef849c0deac3963c49ba93c77 + sha256: dcde459f7bdd30e01c92d23cdc76b5d292cce757ce3a5e37000148eae00a7e69 build: number: 0 From 4a9e87c44bac14878465c3b31f77fdd259dfde86 Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 22 Jul 2024 10:21:00 -0500 Subject: [PATCH 02/13] clean up recipe --- recipes/ms2rescore/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 68ff54cb4ee5e..70e8bd8ad2c1f 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -18,7 +18,7 @@ build: - ms2rescore = ms2rescore.__main__:main - ms2rescore-gui = ms2rescore.gui.__main__:main - ms2rescore-report = ms2rescore.report.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: host: @@ -30,7 +30,7 @@ requirements: - numpy >=1.16.0 - pandas >=1.0 - rich >=12 - - pyteomics >=4.1.0,<=4.6.3 + - pyteomics >=4.7.2 - pyopenms - lxml >=4.5 - ms2pip >=4.0.0-dev8 @@ -40,7 +40,7 @@ requirements: - deeplc >=2.2 - deeplcretrainer >=0.2 - tomli >=2 # [py<311] - - psm-utils >=0.4 + - psm-utils >=0.9 - customtkinter >=5,<6 - mokapot >=0.9 - pydantic >=1.8.2,<2 @@ -51,14 +51,14 @@ requirements: - statsmodels - matplotlib-base - seaborn - - xgboost <2,>=1.3 # from ms2pip + - xgboost >=1.3,<2 # from ms2pip test: imports: - ms2rescore commands: - ms2rescore --help -# - ms2rescore-gui --help +# - ms2rescore-gui --help - ms2rescore-report --help about: From 222a5683c14c653c3ff221b4a37540af61524209 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 30 Jul 2024 23:28:53 -0500 Subject: [PATCH 03/13] add im2deep --- recipes/ms2rescore/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 70e8bd8ad2c1f..2b4f10a43a112 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -18,6 +18,7 @@ build: - ms2rescore = ms2rescore.__main__:main - ms2rescore-gui = ms2rescore.gui.__main__:main - ms2rescore-report = ms2rescore.report.__main__:main + - tims2rescore = ms2rescore.__main__:main_tims script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: @@ -39,18 +40,19 @@ requirements: - cascade-config >=0.4.0 - deeplc >=2.2 - deeplcretrainer >=0.2 - - tomli >=2 # [py<311] + - im2deep >=0.1.3 + - tomli >=2 # [py < 311] - psm-utils >=0.9 - customtkinter >=5,<6 - mokapot >=0.9 - pydantic >=1.8.2,<2 - jinja2 >=3 - plotly >=5 - - sqlalchemy <2,>=1.3 + - sqlalchemy >=1.3,<2 - mokapot - statsmodels - matplotlib-base - - seaborn + - seaborn-base - xgboost >=1.3,<2 # from ms2pip test: From e48bffd37de92cdcf65b4f64fd0791d4634005bf Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Aug 2024 10:13:16 +0000 Subject: [PATCH 04/13] Update ms2rescore to 3.1.1 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 2b4f10a43a112..88746250516b0 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: dcde459f7bdd30e01c92d23cdc76b5d292cce757ce3a5e37000148eae00a7e69 + sha256: 21e9ec8d570490264960e2dd22e763c76c961950024447ce70ede9fbc11eb0aa build: number: 0 From a15dc08f134193a4d52654ac9cf20365883d05c2 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Sep 2024 08:06:55 +0000 Subject: [PATCH 05/13] Update ms2rescore to 3.1.2 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 88746250516b0..cfe56a5a87b79 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.1.1" %} +{% set version = "3.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: 21e9ec8d570490264960e2dd22e763c76c961950024447ce70ede9fbc11eb0aa + sha256: eab5bcd275454fc77c1c99aeb0b1f5e800ce8df3b672840ba5d5fe0b4e8859ae build: number: 0 From 445a0a446eb582eb79cdce4ad17dee7c4dbee5b8 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 1 Oct 2024 15:15:36 +0000 Subject: [PATCH 06/13] Update ms2rescore to 3.1.3 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index cfe56a5a87b79..a43a137b0cf31 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.1.2" %} +{% set version = "3.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: eab5bcd275454fc77c1c99aeb0b1f5e800ce8df3b672840ba5d5fe0b4e8859ae + sha256: 2eb69ed7a488294f419f503bfd652d987cb0f73a6ddaf7f3c44736ad282483a5 build: number: 0 From 7dfcc93e5a9bf0145ff273947177221d4ecc10df Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 2 Oct 2024 09:11:38 +0000 Subject: [PATCH 07/13] Update ms2rescore to 3.1.3.post1 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index a43a137b0cf31..5ee9470b4728c 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.1.3" %} +{% set version = "3.1.3.post1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: 2eb69ed7a488294f419f503bfd652d987cb0f73a6ddaf7f3c44736ad282483a5 + sha256: 432cb82e0ee605f648d2c80a9112a1a19a89d48e7f5a51d6a7bc59f4410cf6cf build: number: 0 From a1c40d19ea640d7465d3a3613b3ba9994ae7aad8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 5 Nov 2024 02:51:28 -0600 Subject: [PATCH 08/13] update dependencies --- recipes/ms2rescore/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 5ee9470b4728c..35759b455e308 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -23,26 +23,26 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - flit-core - pip run: - - python >=3.8 - - numpy >=1.16.0 + - python >=3.9 + - numpy >=1.25.0 - pandas >=1.0 - rich >=12 - pyteomics >=4.7.2 - pyopenms - lxml >=4.5 - - ms2pip >=4.0.0-dev8 + - ms2pip >=4.0.0 - ms2rescore-rs - click >=7 - cascade-config >=0.4.0 - - deeplc >=2.2 - - deeplcretrainer >=0.2 + - deeplc >=3.0,<3.1 + - deeplcretrainer - im2deep >=0.1.3 - tomli >=2 # [py < 311] - - psm-utils >=0.9 + - psm-utils >=1.1 - customtkinter >=5,<6 - mokapot >=0.9 - pydantic >=1.8.2,<2 From 98403383fb6196e570fb05f9030bd0dd2efa1ee0 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 20 Nov 2024 02:53:08 -0600 Subject: [PATCH 09/13] Update meta.yaml --- recipes/ms2rescore/meta.yaml | 36 ++++++++++++++++-------------------- 1 file changed, 16 insertions(+), 20 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 35759b455e308..64515d3f2566b 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -28,31 +28,26 @@ requirements: - pip run: - python >=3.9 - - numpy >=1.25.0 - - pandas >=1.0 - - rich >=12 - - pyteomics >=4.7.2 - - pyopenms - - lxml >=4.5 - - ms2pip >=4.0.0 - - ms2rescore-rs - - click >=7 - cascade-config >=0.4.0 + - click >=7 + - customtkinter >=5,<6 - deeplc >=3.0,<3.1 - deeplcretrainer + - gooey - im2deep >=0.1.3 - - tomli >=2 # [py < 311] - - psm-utils >=1.1 - - customtkinter >=5,<6 - - mokapot >=0.9 - - pydantic >=1.8.2,<2 - jinja2 >=3 + - lxml >=4.5 + - mokapot >=0.10 + - ms2pip >=4.0.0 + - ms2rescore_rs >=0.3.0 + - numpy >=1.25 + - pandas >=1 - plotly >=5 - - sqlalchemy >=1.3,<2 - - mokapot - - statsmodels - - matplotlib-base - - seaborn-base + - psm_utils >=1.1 + - pyopenms >=3.0,<3.2 + - pyteomics >=4.7.2 + - rich >=12 + - tomli >=2 # [py < 311] - xgboost >=1.3,<2 # from ms2pip test: @@ -62,6 +57,7 @@ test: - ms2rescore --help # - ms2rescore-gui --help - ms2rescore-report --help + - tims2rescore --help about: home: https://compomics.github.io/projects/ms2rescore/ @@ -70,7 +66,7 @@ about: license: Apache-2.0 license_family: APACHE license_file: LICENSE - doc_url: https://ms2rescore.readthedocs.io/en/stable/ + doc_url: https://ms2rescore.readthedocs.io/en/stable extra: container: From 52c6ac3a468ce1f11629d2d8ba3f4b0f1dceb60b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 20 Nov 2024 02:56:30 -0600 Subject: [PATCH 10/13] Update meta.yaml --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 64515d3f2566b..ab0813cbb838e 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -39,11 +39,11 @@ requirements: - lxml >=4.5 - mokapot >=0.10 - ms2pip >=4.0.0 - - ms2rescore_rs >=0.3.0 + - ms2rescore-rs - numpy >=1.25 - pandas >=1 - plotly >=5 - - psm_utils >=1.1 + - psm-utils >=1.1 - pyopenms >=3.0,<3.2 - pyteomics >=4.7.2 - rich >=12 From 0df39aa7d790445ffd97dccd3289a779946f188d Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Dec 2024 17:19:52 +0000 Subject: [PATCH 11/13] Update ms2rescore to 3.1.4 --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index ab0813cbb838e..1506467025591 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.1.3.post1" %} +{% set version = "3.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: 432cb82e0ee605f648d2c80a9112a1a19a89d48e7f5a51d6a7bc59f4410cf6cf + sha256: 1b87a6c9991333eee83001d519d7378eabf8b84f1474abb2d9be1b87819c67f1 build: number: 0 From 08d5f96e4570b465ec148981041b21db2ce90e04 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 21 Jan 2025 16:49:14 -0600 Subject: [PATCH 12/13] Update meta.yaml --- recipes/ms2rescore/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 1506467025591..2ef141f8ae0cb 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -60,17 +60,18 @@ test: - tims2rescore --help about: - home: https://compomics.github.io/projects/ms2rescore/ + home: https://compomics.github.io/projects/ms2rescore summary: 'MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.' dev_url: https://github.com/compomics/ms2rescore license: Apache-2.0 license_family: APACHE license_file: LICENSE doc_url: https://ms2rescore.readthedocs.io/en/stable + dev_url: https://github.com/compomics/ms2rescore extra: container: # Click requires the extended container - extended-base: true + extended-base: True recipe-maintainers: - compomics From 1809370b12cd9d333a2d1dc5127ef289c14476c6 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 21 Jan 2025 19:11:34 -0600 Subject: [PATCH 13/13] Update meta.yaml --- recipes/ms2rescore/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 2ef141f8ae0cb..5ccf9715a28b5 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -62,7 +62,6 @@ test: about: home: https://compomics.github.io/projects/ms2rescore summary: 'MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.' - dev_url: https://github.com/compomics/ms2rescore license: Apache-2.0 license_family: APACHE license_file: LICENSE