34 convert distribution system from poetry to uv (#35)

* chore: convert from poetry to uv

* chore: convert poetry to uv in github action

* fix: use specific uv venv

* fix: install uv manually

* fix: create a venv with uv

* fix: use dot notation in imports with main

* fix: remove dot notation and call from package directly

* fix: add all namespaces to __all__ in __init__

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: formatting

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* chore: troubleshooting CI

* docs: update readme with table

* chore: bump minor version, potential breaking changes with installation

.github/workflows/CI.yml

@@ -1,11 +1,13 @@
-name: Python Package using Conda
+name: Python Package CI
 
 on: [push]
 
 jobs:
-
   ci:
-    needs: [ostest, full-ci]
+    needs: [
+      ostest, 
+      full-ci,
+    ]
     name: CI
     runs-on: 'ubuntu-latest'
     steps:
@@ -17,65 +19,65 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [ "3.9", "3.10", "3.11" ]
+        python-version: ["3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v4
 
-      - name: Install poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
         run: |
-          pip install poetry
+          uv python install ${{ matrix.python-version }}
+          uv venv  
 
       - name: Install project
         run: |
-          poetry install
+          uv sync --all-extras --dev
+          uv tool install .
 
       - name: Test with pytest
         run: |
-          poetry run pytest -v
+          uv run pytest -v
 
       - name: Test table io from commandline
         run: |
-          poetry run geomux -i example/example.tsv.gz -o results_table.tab
+          uvx geomux -i example/example.tsv.gz -o results_table.tab
 
       - name: Test adat io from commandline
         run: |
-          poetry run geomux -i example/example.h5ad -o results_table.tab
+          uvx geomux -i example/example.h5ad -o results_table.tab
 
   ostest:
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 5
       matrix:
-        os: [ "windows-latest", "macos-latest" ]
+        os: ["windows-latest", "macos-latest"]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.11
+    - uses: actions/checkout@v4
 
-    - name: Install poetry
-      run: |
-        pip install poetry
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
+    - name: Set up Python 3.11
+      run: uv python install 3.11
 
     - name: Install project
       run: |
-        poetry install
+        uv sync --all-extras --dev
+        uv tool install .
 
     - name: Test with pytest
       run: |
-        poetry run pytest -v
+        uv run pytest -v
 
     - name: Test table io from commandline
       run: |
-        poetry run geomux -i example/example.tsv.gz -o results_table.tab
+        uvx geomux -i example/example.tsv.gz -o results_table.tab
 
     - name: Test adat io from commandline
       run: |
-        poetry run geomux -i example/example.h5ad -o results_table.tab
+        uvx geomux -i example/example.h5ad -o results_table.tab

.python-version

@@ -0,0 +1 @@
+3.11

README.md

@@ -97,17 +97,15 @@ observations as there are input cells.
 
 The columns of this dataframe will include:
 
-- cell_id
-    - The name of the cell provided or the index.
-- assignment
-    - A list representing all significant guides within that cell.
-- moi
-    - The number of significant guides within the cell.
-- n_umi
-    - The number of UMIs observed in the cell.
-- p_value
-    - The adjusted p-value of the hypergeometric test for that cell/guide test.
-- log_odds
-    - The log odds of observing the highest scoring guide compared to the second highest.
-- tested
-    - A bool flag representing whether the cell was included in the test (or `False` if it was filtered for low UMI counts)
+| Column Name | Description |
+| ----------- | ----------- |
+| cell_id | The name of the cell provided or the index. |
+| assignment | A list representing all significant guides within that cell. |
+| counts | The number of UMIs observed in the cell. |
+| pvalues | The adjusted p-value of the hypergeometric test for that cell/guide test. |
+| log_odds | The log odds of observing the highest scoring guide compared to the second highest. |
+| moi | The number of significant guides within the cell. |
+| n_umi | The number of UMIs observed in the cell. |
+| min_pvalue | The minimum pvalue across all significant guides within the cell. |
+| max_count | The maximum count across all significant guides within the cell. |
+| tested | A bool flag representing whether the cell was included in the test (or `False` if it was filtered for low UMI counts) |

geomux/__init__.py

@@ -1,5 +1,8 @@
 from .geomux import Geomux
-from .utils import read_table, read_anndata
+from .utils import read_anndata, read_table
+
+__all__ = ["Geomux", "read_table", "read_anndata"]
+
 import logging
 
 logging.basicConfig(

geomux/__main__.py

@@ -1,6 +1,7 @@
-import sys
 import argparse
-from geomux import Geomux, read_table, read_anndata
+import sys
+
+from geomux import Geomux, read_anndata, read_table
 
 
 def get_args():

pyproject.toml

@@ -1,27 +1,22 @@
-[tool.poetry]
+[project]
 name = "geomux"
-version = "0.2.10"
+version = "0.3.0"
 description = "A tool to assign identifiers to cell barcodes"
-authors = ["Noam Teyssier"]
-license = "MIT"
+authors = [{ name = "Noam Teyssier" }]
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
 readme = "README.md"
+dependencies = [
+  "adjustpy>=0.1.1",
+  "anndata>=0.10.9",
+  "numpy>=2.1.1",
+  "pandas>=2.2.3",
+  "scipy>=1.14.1",
+]
 
-[tool.poetry.scripts]
-geomux = 'geomux.__main__:main_cli'
+[project.scripts]
+geomux = "geomux.__main__:main_cli"
 
-[tool.poetry.dependencies]
-python = ">=3.9,<3.13"
-numpy = "^1.24.0"
-pandas = "^2.0.3"
-anndata = "^0.9.1"
-scipy = "^1.11.1"
-adjustpy = "^0.1.1"
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
-muxsim = "^0.1.0"
-black = "^23.3.0"
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.uv]
+dev-dependencies = ["pytest>=8.3.3", "muxsim>=0.1.0", "black>=24.8.0"]
+package = true