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Add Instanovo #51796

Merged
merged 24 commits into from
Nov 19, 2024
Merged

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
87ba17a
make numpy version a lower bound
BioGeek Nov 14, 2024
2587292
Dropping all bounds
BioGeek Nov 16, 2024
c7c05e4
Explicitly add pytorch-gpu
BioGeek Nov 16, 2024
7f423f2
Add packges which `pip check` complained about
BioGeek Nov 16, 2024
217a56f
remove `pip check`, `pytorch-gpu`, `rdkit`, `lxml`, and `scipy` from …
BioGeek Nov 17, 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") }}

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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 >=0.28.0
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⚠️ Potential issue

Critical: Unavailable dependencies in conda channels

The following dependencies are not available in conda-forge or bioconda channels:

  • matchms
  • pyopenms
  • spectrum_utils

These packages need to be added to conda-forge first. Until then, consider:

  1. Submitting feedstock PRs for these packages to conda-forge
  2. Or using PyPI fallback for these specific packages

Would you like assistance in creating conda-forge feedstock PRs for these packages?

Also applies to: 37-37, 42-42

- neptune >=1.12.0
- numpy ==2.1.0rc1
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⚠️ Potential issue

Update numpy version constraint.

Using a release candidate version (2.1.0rc1) in production is risky. Consider using a stable version:

-    - numpy ==2.1.0rc1
+    - numpy >=2.0.0
📝 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
- numpy ==2.1.0rc1
- 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 >=2.4.1
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⚠️ Potential issue

Update PyTorch and CUDA configuration

Current issues:

  1. pytorch version >=2.4.1 is not yet available
  2. cudatoolkit should have a version constraint
  3. Consider making CUDA optional for CPU-only installations

Recommendations:

  1. Use a more conservative PyTorch version that's available in conda-forge
  2. Add version constraint for cudatoolkit
  3. Consider splitting into CPU/GPU variants

Apply this diff to update the configuration:

-    - pytorch >=2.4.1
-    - cudatoolkit
+    - pytorch >=2.0.0
+    - cudatoolkit >=11.8

Also applies to: 46-46

- 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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