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forcing more versions for compatibility. #35

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merged 16 commits into from
Nov 23, 2024
Merged

forcing more versions for compatibility. #35

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450f503
forcing more versions for compatibility.
ypriverol Nov 22, 2024
0c5d3c9
forcing more versions
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forcing more versions
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2a2d103
forcing more versions for compatibility.
ypriverol Nov 22, 2024
7002247
Merge remote-tracking branch 'origin/dev' into dev
ypriverol Nov 22, 2024
640af8f
forcing more versions
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forcing more versions
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forcing more versions
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forcing more versions
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forcing more versions
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forcing more versions
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forcing more versions
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Merge remote-tracking branch 'origin/dev' into dev
ypriverol Nov 23, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/conda-build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: |
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2 changes: 1 addition & 1 deletion .github/workflows/python-package.yml
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Expand Up @@ -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
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3 changes: 3 additions & 0 deletions environment.yml
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Expand Up @@ -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
7 changes: 5 additions & 2 deletions pyproject.toml
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Expand Up @@ -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 <[email protected]>",
"Dai Chengxin <[email protected]>",
Expand All @@ -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 = "*"
Expand All @@ -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"
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2 changes: 1 addition & 1 deletion quantmsutils/__init__.py
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@@ -1 +1 @@
__version__ = "0.0.14"
__version__ = "0.0.15"
11 changes: 7 additions & 4 deletions recipe/meta.yaml
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@@ -1,7 +1,7 @@
# recipe/meta.yaml
package:
name: quantms-utils
version: "0.0.14"
version: "0.0.15"

source:
path: ../
Expand All @@ -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
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test:
imports:
- quantmsutils
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3 changes: 3 additions & 0 deletions requirements.txt
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Expand Up @@ -7,3 +7,6 @@ numpy
pyarrow
deepLC==2.2.38
psm-utils==0.8.3
scipy==1.13.1
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💡 Codebase verification

Version compatibility constraints need attention

The verification reveals important compatibility requirements:

  • scipy 1.13.1 requires numpy>=1.22.4 and <2.3
  • Current requirements.txt has unpinned numpy version
  • No Python version constraints are specified

To ensure reliable builds:

  • Pin numpy to a compatible version: numpy>=1.22.4,<2.3
  • Add Python version constraint: python>=3.9 (scipy 1.13.1 requirement)
  • Consider pinning other scientific dependencies to avoid conflicts
🔗 Analysis chain

Verify scipy version compatibility with other dependencies

The addition of scipy==1.13.1 requires careful consideration of compatibility with other scientific computing packages in the requirements.

Let's verify the compatibility matrix:

Let me gather more information about the numpy version in requirements.txt to ensure compatibility.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check compatibility between scipy and other dependencies

# Check if numpy version is specified in other config files
echo "Checking for numpy version specifications..."
rg -l "numpy[=><]" --type yaml --type toml

# Check scipy 1.13.1 requirements from PyPI
echo "Checking scipy 1.13.1 requirements..."
curl -s https://pypi.org/pypi/scipy/1.13.1/json | jq -r '.info.requires_dist[]'

Length of output: 1241

Script:

#!/bin/bash
# Check numpy version in requirements.txt
echo "Checking numpy version in requirements.txt..."
rg "^numpy" requirements.txt

# Check if there's any Python version constraint
echo "Checking for Python version constraints..."
rg "^python" requirements.txt

Length of output: 264

pygam
protobuf==3.19.6
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