From 08b287717faed69b2cfc9728dc07b14faf227772 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Tue, 22 Oct 2024 15:59:47 +0200 Subject: [PATCH 01/19] Add `instanovo` recipe --- recipes/instanovo/meta.yaml | 64 +++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 recipes/instanovo/meta.yaml diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml new file mode 100644 index 0000000000000..29d1bf2ddcd1a --- /dev/null +++ b/recipes/instanovo/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "instanovo" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/instanovo-{{ version }}.tar.gz + sha256: fd9cfc377d9f8da5272f96b2eb4c14c08b579d7a65466aa402601ec6c4b42672 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x") }} + + +requirements: + host: + - python >=3.10,<3.12 + - setuptools >=69.1.1 + - pip + run: + - python >=3.10,<3.12 + - click >=8.1.7 + - datasets >=3.0.1 + - hydra-core >=1.3.2 + - jaxtyping >=0.2.34 + - jiwer >=3.0.4 + - matchms >=0.27.0 + - neptune >=1.12.0 + - numpy >=1.26.4 + - omegaconf >=2.3.0 + - pandas >=2.2.3 + - polars >=1.9.0 + - pyopenms >=3.1.0 # TODO change to 3.2.0 when available, see https://github.com/bioconda/bioconda-recipes/pull/51014 + - python-dotenv >=1.0.1 + - pytorch-lightning >=2.4.0 + - s3fs >=2024.6.1 + - scikit-learn >=1.5.2 + - spectrum_utils >=0.4.2 + - tensorboard >=2.18.0 + - pytorch-gpu >=2.4.1 + - tqdm >=4.66.5 + +test: + imports: + - instanovo + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/instadeepai/instanovo + summary: De novo peptide sequencing with InstaNovo + license: Apache-2.0 + license_file: LICENSE.md + +extra: + recipe-maintainers: + - BioGeek From 6c34a7187a04a5751e65fc3f07244e62100c3ef4 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Tue, 22 Oct 2024 16:35:56 +0200 Subject: [PATCH 02/19] Add TODO comments --- recipes/instanovo/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 29d1bf2ddcd1a..a16f07ceed834 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -29,20 +29,20 @@ requirements: - hydra-core >=1.3.2 - jaxtyping >=0.2.34 - jiwer >=3.0.4 - - matchms >=0.27.0 + - matchms >=0.27.0 # TODO depends on https://github.com/bioconda/bioconda-recipes/pull/51552 being merged - neptune >=1.12.0 - numpy >=1.26.4 - omegaconf >=2.3.0 - pandas >=2.2.3 - polars >=1.9.0 - - pyopenms >=3.1.0 # TODO change to 3.2.0 when available, see https://github.com/bioconda/bioconda-recipes/pull/51014 + - pyopenms >=3.2.0 # TODO depends on https://github.com/bioconda/bioconda-recipes/pull/51014 - python-dotenv >=1.0.1 - pytorch-lightning >=2.4.0 - s3fs >=2024.6.1 - scikit-learn >=1.5.2 - spectrum_utils >=0.4.2 - tensorboard >=2.18.0 - - pytorch-gpu >=2.4.1 + - pytorch >=2.4.1 - tqdm >=4.66.5 test: @@ -50,6 +50,8 @@ test: - instanovo commands: - pip check + - instanovo --version + - python -c "import instanovo; print(instanovo.__version__)" requires: - pip From cf1a46cdc5f323c64f4d81ae7db5155b2e60c9dd Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Tue, 22 Oct 2024 23:04:48 +0200 Subject: [PATCH 03/19] dependencies of matchms have been updated --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index a16f07ceed834..3c44b6d4f3977 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -29,7 +29,7 @@ requirements: - hydra-core >=1.3.2 - jaxtyping >=0.2.34 - jiwer >=3.0.4 - - matchms >=0.27.0 # TODO depends on https://github.com/bioconda/bioconda-recipes/pull/51552 being merged + - matchms >=0.27.0 - neptune >=1.12.0 - numpy >=1.26.4 - omegaconf >=2.3.0 From 04119e086acf272d49c2e16c85dbd911a6b92bb0 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Tue, 29 Oct 2024 16:39:33 +0200 Subject: [PATCH 04/19] Remove duplicate python lines, remove uper version bound --- recipes/instanovo/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 3c44b6d4f3977..9826235b2ede7 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -19,11 +19,10 @@ build: requirements: host: - - python >=3.10,<3.12 + - python >=3.10 - setuptools >=69.1.1 - pip run: - - python >=3.10,<3.12 - click >=8.1.7 - datasets >=3.0.1 - hydra-core >=1.3.2 @@ -35,7 +34,7 @@ requirements: - omegaconf >=2.3.0 - pandas >=2.2.3 - polars >=1.9.0 - - pyopenms >=3.2.0 # TODO depends on https://github.com/bioconda/bioconda-recipes/pull/51014 + - pyopenms >=3.2.0 - python-dotenv >=1.0.1 - pytorch-lightning >=2.4.0 - s3fs >=2024.6.1 @@ -50,7 +49,6 @@ test: - instanovo commands: - pip check - - instanovo --version - python -c "import instanovo; print(instanovo.__version__)" requires: - pip From 3bcc1d482c5e723b2b452745459a1174f38fe290 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Wed, 30 Oct 2024 00:47:41 +0200 Subject: [PATCH 05/19] Add upper python bound again --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 9826235b2ede7..f8ae0d112bf71 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -19,7 +19,7 @@ build: requirements: host: - - python >=3.10 + - python >=3.10,<3.12 - setuptools >=69.1.1 - pip run: From 6e0da4540b0eacf42c0bd491ed7171cb40af9105 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Wed, 30 Oct 2024 01:13:08 +0200 Subject: [PATCH 06/19] unpin all packages --- recipes/instanovo/meta.yaml | 40 ++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index f8ae0d112bf71..78da7f197e5e1 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -23,26 +23,26 @@ requirements: - setuptools >=69.1.1 - pip run: - - click >=8.1.7 - - datasets >=3.0.1 - - hydra-core >=1.3.2 - - jaxtyping >=0.2.34 - - jiwer >=3.0.4 - - matchms >=0.27.0 - - neptune >=1.12.0 - - numpy >=1.26.4 - - omegaconf >=2.3.0 - - pandas >=2.2.3 - - polars >=1.9.0 - - pyopenms >=3.2.0 - - python-dotenv >=1.0.1 - - pytorch-lightning >=2.4.0 - - s3fs >=2024.6.1 - - scikit-learn >=1.5.2 - - spectrum_utils >=0.4.2 - - tensorboard >=2.18.0 - - pytorch >=2.4.1 - - tqdm >=4.66.5 + - click + - datasets + - hydra-core + - jaxtyping + - jiwer + - matchms + - neptune + - numpy + - omegaconf + - pandas + - polars + - pyopenms + - python-dotenv + - pytorch-lightning + - s3fs + - scikit-learn + - spectrum_utils + - tensorboard + - pytorch + - tqdm test: imports: From f6a93d4147493dc3ce6938bc484121efe541782f Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Wed, 30 Oct 2024 01:32:47 +0200 Subject: [PATCH 07/19] re-add pinned packages, add eigen, add doi --- recipes/instanovo/meta.yaml | 43 ++++++++++++++++++++----------------- 1 file changed, 23 insertions(+), 20 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 78da7f197e5e1..1959da07d2736 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -23,26 +23,27 @@ requirements: - setuptools >=69.1.1 - pip run: - - click - - datasets - - hydra-core - - jaxtyping - - jiwer - - matchms - - neptune - - numpy - - omegaconf - - pandas - - polars - - pyopenms - - python-dotenv - - pytorch-lightning - - s3fs - - scikit-learn - - spectrum_utils - - tensorboard - - pytorch - - tqdm + - click >=8.1.7 + - datasets >=3.0.1 + - hydra-core >=1.3.2 + - jaxtyping >=0.2.34 + - jiwer >=3.0.4 + - matchms >=0.27.0 + - neptune >=1.12.0 + - numpy >=1.23,<1.27 + - omegaconf >=2.3.0 + - pandas >=2.2.3 + - polars >=1.9.0 + - pyopenms >=3.2.0 + - python-dotenv >=1.0.1 + - pytorch-lightning >=2.4.0 + - s3fs >=2024.6.1 + - scikit-learn >=1.5.2 + - spectrum_utils >=0.4.2 + - tensorboard >=2.18.0 + - pytorch >=2.4.1 + - tqdm >=4.66.5 + - eigen >=3.3.4 test: imports: @@ -62,3 +63,5 @@ about: extra: recipe-maintainers: - BioGeek + identifiers: + - doi:10.1101/2023.08.30.555055 From 3d9b497890578de64208d5a0494525ca2eed1bea Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Wed, 30 Oct 2024 01:42:12 +0200 Subject: [PATCH 08/19] remove eigen, use pytorch-gpu --- recipes/instanovo/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 1959da07d2736..89e6d1fa1bb25 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -41,9 +41,8 @@ requirements: - scikit-learn >=1.5.2 - spectrum_utils >=0.4.2 - tensorboard >=2.18.0 - - pytorch >=2.4.1 + - pytorch-gpu >=2.4.1 - tqdm >=4.66.5 - - eigen >=3.3.4 test: imports: From 28477ca20c7731a87abbf634933e28a35f867e47 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 09:34:47 +0000 Subject: [PATCH 09/19] Update recipes/instanovo/meta.yaml --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 89e6d1fa1bb25..1dcd1330321d2 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -28,7 +28,7 @@ requirements: - hydra-core >=1.3.2 - jaxtyping >=0.2.34 - jiwer >=3.0.4 - - matchms >=0.27.0 + - matchms >=0.28.1 - neptune >=1.12.0 - numpy >=1.23,<1.27 - omegaconf >=2.3.0 From a5bff4f0198c49ce1b3c64553f05b1dd6157648c Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 09:34:57 +0000 Subject: [PATCH 10/19] Update recipes/instanovo/meta.yaml --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 1dcd1330321d2..de672c5a0c8f8 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -30,7 +30,7 @@ requirements: - jiwer >=3.0.4 - matchms >=0.28.1 - neptune >=1.12.0 - - numpy >=1.23,<1.27 + - numpy >=2.0.0 - omegaconf >=2.3.0 - pandas >=2.2.3 - polars >=1.9.0 From ac53d1807575c73d33586a7035a155fec89b50a3 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 13:25:58 +0000 Subject: [PATCH 11/19] Update meta.yaml --- recipes/instanovo/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index de672c5a0c8f8..20f1e6b176da7 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -43,6 +43,7 @@ requirements: - tensorboard >=2.18.0 - pytorch-gpu >=2.4.1 - tqdm >=4.66.5 + - cudatoolkit test: imports: From 0fbcd018506f1c0b128839095b5571023f9a647a Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Thu, 7 Nov 2024 16:36:15 +0200 Subject: [PATCH 12/19] Bump version of matchms to 0.28.0 Add TODO comments dependencies of matchms have been updated Remove duplicate python lines, remove uper version bound Add upper python bound again unpin all packages re-add pinned packages, add eigen, add doi remove eigen, use pytorch-gpu Bump version of matchms to 0.28.0 --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 20f1e6b176da7..99d37709b838d 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -28,7 +28,7 @@ requirements: - hydra-core >=1.3.2 - jaxtyping >=0.2.34 - jiwer >=3.0.4 - - matchms >=0.28.1 + - matchms >=0.28.0 - neptune >=1.12.0 - numpy >=2.0.0 - omegaconf >=2.3.0 From 01c40d1b6758b4c5585b0c96b8356b83bd7a0dd6 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Thu, 7 Nov 2024 16:52:49 +0200 Subject: [PATCH 13/19] Use pytorch instead of pytorch-gpu --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 99d37709b838d..6d93611ae1870 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -41,7 +41,7 @@ requirements: - scikit-learn >=1.5.2 - spectrum_utils >=0.4.2 - tensorboard >=2.18.0 - - pytorch-gpu >=2.4.1 + - pytorch >=2.4.1 - tqdm >=4.66.5 - cudatoolkit From 177596f1a0aa752184dd92f2d5ab4dc019d04cc5 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 7 Nov 2024 15:32:15 +0000 Subject: [PATCH 14/19] Update meta.yaml --- recipes/instanovo/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 6d93611ae1870..620b321d926e6 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -30,7 +30,7 @@ requirements: - jiwer >=3.0.4 - matchms >=0.28.0 - neptune >=1.12.0 - - numpy >=2.0.0 + - numpy ==2.1.0rc1 - omegaconf >=2.3.0 - pandas >=2.2.3 - polars >=1.9.0 From 87ba17a2dc990b49cfd96fbf298258ad567ee934 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Thu, 14 Nov 2024 16:14:32 +0200 Subject: [PATCH 15/19] make numpy version a lower bound --- recipes/instanovo/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 620b321d926e6..6d8115727aca6 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -30,7 +30,7 @@ requirements: - jiwer >=3.0.4 - matchms >=0.28.0 - neptune >=1.12.0 - - numpy ==2.1.0rc1 + - numpy >=2.1.0rc1 - omegaconf >=2.3.0 - pandas >=2.2.3 - polars >=1.9.0 @@ -43,7 +43,6 @@ requirements: - tensorboard >=2.18.0 - pytorch >=2.4.1 - tqdm >=4.66.5 - - cudatoolkit test: imports: From 2587292cfe10a96ce5e61aee2ca4571f0d7820e2 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Sat, 16 Nov 2024 21:51:32 +0200 Subject: [PATCH 16/19] Dropping all bounds --- recipes/instanovo/meta.yaml | 40 ++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 6d8115727aca6..328999872fd09 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -23,26 +23,26 @@ requirements: - setuptools >=69.1.1 - pip run: - - click >=8.1.7 - - datasets >=3.0.1 - - hydra-core >=1.3.2 - - jaxtyping >=0.2.34 - - jiwer >=3.0.4 - - matchms >=0.28.0 - - neptune >=1.12.0 - - numpy >=2.1.0rc1 - - omegaconf >=2.3.0 - - pandas >=2.2.3 - - polars >=1.9.0 - - pyopenms >=3.2.0 - - python-dotenv >=1.0.1 - - pytorch-lightning >=2.4.0 - - s3fs >=2024.6.1 - - scikit-learn >=1.5.2 - - spectrum_utils >=0.4.2 - - tensorboard >=2.18.0 - - pytorch >=2.4.1 - - tqdm >=4.66.5 + - click + - datasets + - hydra-core + - jaxtyping + - jiwer + - matchms + - neptune + - numpy + - omegaconf + - pandas + - polars + - pyopenms + - python-dotenv + - pytorch-lightning + - s3fs + - scikit-learn + - spectrum_utils + - tensorboard + - pytorch + - tqdm test: imports: From c7c05e40616cb55826a6f32c87dbd113075a45ce Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Sat, 16 Nov 2024 21:56:47 +0200 Subject: [PATCH 17/19] Explicitly add pytorch-gpu See this announcement: https://dev-discuss.pytorch.org/t/pytorch-deprecation-of-conda-nightly-builds/2590 --- recipes/instanovo/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 328999872fd09..b6f333658c480 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -43,6 +43,7 @@ requirements: - tensorboard - pytorch - tqdm + - pytorch-gpu test: imports: From 7f423f2634ec173009a39ce62e330e17f4d915d6 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Sat, 16 Nov 2024 22:11:22 +0200 Subject: [PATCH 18/19] Add packges which `pip check` complained about --- recipes/instanovo/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index b6f333658c480..9ca5e2ca91a09 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -44,6 +44,9 @@ requirements: - pytorch - tqdm - pytorch-gpu + - rdkit + - lxml + - scipy test: imports: From 217a56f43b28a2d41a82b1ab952b0884c860bb67 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Sun, 17 Nov 2024 21:16:45 +0200 Subject: [PATCH 19/19] remove `pip check`, `pytorch-gpu`, `rdkit`, `lxml`, and `scipy` from `requirements` in `meta.yaml` --- recipes/instanovo/meta.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml index 9ca5e2ca91a09..a81bac3f6af7b 100644 --- a/recipes/instanovo/meta.yaml +++ b/recipes/instanovo/meta.yaml @@ -43,16 +43,11 @@ requirements: - tensorboard - pytorch - tqdm - - pytorch-gpu - - rdkit - - lxml - - scipy test: imports: - instanovo commands: - - pip check - python -c "import instanovo; print(instanovo.__version__)" requires: - pip