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Add Instanovo #51796

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Add Instanovo #51796

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08b2877
Add `instanovo` recipe
BioGeek Oct 22, 2024
6c34a71
Add TODO comments
BioGeek Oct 22, 2024
cf1a46c
dependencies of matchms have been updated
BioGeek Oct 22, 2024
04119e0
Remove duplicate python lines, remove uper version bound
BioGeek Oct 29, 2024
3bcc1d4
Add upper python bound again
BioGeek Oct 29, 2024
d846578
Merge branch 'master' into instanovo
BioGeek Oct 29, 2024
6e0da45
unpin all packages
BioGeek Oct 29, 2024
f6a93d4
re-add pinned packages, add eigen, add doi
BioGeek Oct 29, 2024
3d9b497
remove eigen, use pytorch-gpu
BioGeek Oct 29, 2024
5b33ce3
Merge branch 'master' into instanovo
BioGeek Oct 30, 2024
26ddf5a
Merge branch 'master' into instanovo
BioGeek Oct 31, 2024
9c2b661
Merge branch 'master' into instanovo
hechth Nov 7, 2024
28477ca
Update recipes/instanovo/meta.yaml
hechth Nov 7, 2024
a5bff4f
Update recipes/instanovo/meta.yaml
hechth Nov 7, 2024
92e9668
Merge branch 'master' into instanovo
hechth Nov 7, 2024
ac53d18
Update meta.yaml
hechth Nov 7, 2024
0fbcd01
Bump version of matchms to 0.28.0
BioGeek Nov 7, 2024
01c40d1
Use pytorch instead of pytorch-gpu
BioGeek Nov 7, 2024
177596f
Update meta.yaml
hechth Nov 7, 2024
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67 changes: 67 additions & 0 deletions recipes/instanovo/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
{% 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") }}
Comment on lines +16 to +17
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🛠️ Refactor suggestion

Remove unnecessary run_exports section

The run_exports section is typically used for C/C++ libraries to ensure ABI compatibility. For a pure Python package (noarch: python), this section is unnecessary and could cause unintended version pinning issues.

Apply this diff to remove the section:

 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") }}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
run_exports:
- {{ pin_subpackage(name | lower, max_pin="x.x") }}
build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0


Comment on lines +12 to +18
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🛠️ Refactor suggestion

Remove unnecessary run_exports section.

The run_exports section is typically used for C/C++ libraries to ensure ABI compatibility. For a pure Python package (noarch: python), this section is unnecessary and could cause unintended version pinning issues.

Apply this diff to remove the section:

 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") }}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
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") }}
build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0


requirements:
host:
- python >=3.10,<3.12
- 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 >=0.28.1
- neptune >=1.12.0
- numpy >=2.0.0
- 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-gpu >=2.4.1
- tqdm >=4.66.5
- cudatoolkit

test:
imports:
- instanovo
commands:
- pip check
- python -c "import instanovo; print(instanovo.__version__)"
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
identifiers:
- doi:10.1101/2023.08.30.555055
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