rebase

.github/CODEOWNERS

@@ -1,3 +1,3 @@
 # For more information see:
 # https://help.github.com/en/github/creating-cloning-and-archiving-repositories/about-code-owners
-* @recursionpharma/cartography
+* @recursionpharma/cartography

.github/workflows/publish.yaml

@@ -0,0 +1,30 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build --sdist --wheel
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/quality.yaml

@@ -0,0 +1,18 @@
+name: Quality
+on: [push]
+jobs:
+  tests:
+    name: Quality
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: update pip
+        run: |
+          pip install -U wheel
+          pip install -U setuptools
+          python -m pip install -U pip
+      - run: pip install tox
+      - run: tox -e style

.github/workflows/test.yaml

@@ -0,0 +1,44 @@
+name: Test
+on: [push]
+jobs:
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        minor_version: [8, 9, 10, 11]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        exclude:
+        # exclude Windows on Python 3.8 due to Jaxlib incompatibility
+        # (might be able to fix by using system-dependent lockfile, but not worth our time)
+        - os: windows-latest
+          minor_version: 8
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.${{ matrix.minor_version }}
+      - name: update pip
+        run: |
+          pip install -U wheel
+          pip install -U setuptools
+          python -m pip install -U pip
+      - run: pip install tox
+      - run: tox -e py3${{ matrix.minor_version }}
+      - uses: actions/upload-artifact@v3
+        with:
+          name: coverage.${{ matrix.os }}.py3${{ matrix.minor_version }}
+          path: ./.coverage.py3${{ matrix.minor_version }}
+  # coverage:
+  #   needs: tests
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - uses: actions/download-artifact@v3
+  #       with:
+  #         path: .
+  #     - run: pip install coverage
+  #     - run: |
+  #         coverage combine coverage*/
+  #         coverage report --fail-under=0

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 #   pre-commit autoupdate
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-added-large-files
     -   id: detect-private-key
@@ -19,45 +19,41 @@ repos:
     -   id: mixed-line-ending
     -   id: end-of-file-fixer
 
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-    -   id: seed-isort-config
 -   repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
     -   id: isort
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.15.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
 
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.6.1
     hooks:
     -   id: mypy
         args: [--ignore-missing-imports, --python-version=3.8, --install-types, --non-interactive]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: '6.0.0'
+    rev: '6.1.0'
     hooks:
     -   id: flake8
 
 -   repo: https://github.com/PyCQA/bandit
-    rev: '1.7.4'
+    rev: '1.7.5'
     hooks:
     -   id: bandit
         exclude: tests/.*$
 
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.10.1
     hooks:
     - id: black
       language_version: python3.8
 
 -   repo: https://github.com/abravalheri/validate-pyproject
-    rev: main
+    rev: v0.15
     hooks:
       - id: validate-pyproject

MANIFEST.in

@@ -1 +1 @@
-include efaar_benchmarking/benchmark_annotations/*
+include efaar_benchmarking/benchmark_annotations/*

README.md

@@ -1,7 +1,7 @@
 # EFAAR_benchmarking
 
 This library enables computation and retrieval of metrics to benchmark a whole-genome perturbative map created by the pipeline.
-Metrics that can be computed using this repo are pairwise gene-gene recall for the reactome, corum, and humap datasets which 
+Metrics that can be computed using this repo are pairwise gene-gene recall for the reactome, corum, and humap datasets which
 are publicly available.
 
 By default, we do not filter on perturbation fingerprint, although filtering is available through the parameters to the `benchmark` function.

VERSION

@@ -1,2 +1,2 @@
 MAJOR="0"
-MINOR="0"
+MINOR="1"

efaar_benchmarking/data_loading.py

@@ -3,7 +3,6 @@
 import scanpy as sc
 import numpy as np
 
-
 def load_replogle(gene_type, data_type, data_path="data/"):
     """
     Load Replogle et al. 2020 single-cell RNA-seq data for K562 cells.

efaar_benchmarking/efaar.py

@@ -1,10 +1,11 @@
 import numpy as np
 import pandas as pd
-import efaar_benchmarking.constants as cst
-from scvi.model import SCVI
 import scanpy as sc
+from scvi.model import SCVI
 from sklearn.utils import Bunch
 
+import efaar_benchmarking.constants as cst
+
 
 def embed_by_scvi(adata, BATCH_KEY="gem_group", N_LATENT=128, N_HIDDEN=256):
     """

efaar_benchmarking/utils.py

@@ -1,9 +1,11 @@
-from sklearn.utils import Bunch
-from sklearn.metrics.pairwise import cosine_similarity
-import efaar_benchmarking.constants as cst
+from typing import Optional
+
 import numpy as np
 import pandas as pd
-from typing import Optional
+from sklearn.metrics.pairwise import cosine_similarity
+from sklearn.utils import Bunch
+
+import efaar_benchmarking.constants as cst
 
 
 def compute_process_cosine_sim(

pyproject.toml

@@ -46,18 +46,20 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-	"bandit",
+	"bandit[toml]",
 	"black",
 	"coverage",
 	"docstr-coverage",
 	"flake8",
+	"isort",
 	"mypy",
 	"pre-commit",
 	"pytest",
 	"pytest-cov",
 	"pyupgrade",
 	"radon",
 	"types-pkg_resources",
+	"types-setuptools",
 	"tox",
 	"validate-pyproject[all]",
 	"jupyterlab",

requirements/dev_3.10.txt

@@ -59,13 +59,13 @@ backcall==0.2.0
     # via ipython
 backoff==2.2.1
     # via lightning
-bandit==1.7.5
+bandit[toml]==1.7.5
     # via efaar-benchmarking (pyproject.toml)
 beautifulsoup4==4.12.2
     # via
     #   lightning
     #   nbconvert
-black==23.10.0
+black==23.10.1
     # via efaar-benchmarking (pyproject.toml)
 bleach==6.1.0
     # via nbconvert
@@ -187,18 +187,37 @@ fsspec[http]==2023.10.0
     #   pytorch-lightning
     #   s3fs
     #   torch
-gcsfs==0.8.0
+gcsfs==2023.10.0
     # via efaar-benchmarking (pyproject.toml)
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.40
     # via bandit
+google-api-core==2.12.0
+    # via
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth==2.23.3
     # via
     #   gcsfs
+    #   google-api-core
     #   google-auth-oauthlib
+    #   google-cloud-core
+    #   google-cloud-storage
 google-auth-oauthlib==1.1.0
     # via gcsfs
+google-cloud-core==2.3.3
+    # via google-cloud-storage
+google-cloud-storage==2.12.0
+    # via gcsfs
+google-crc32c==1.5.0
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
+google-resumable-media==2.6.0
+    # via google-cloud-storage
+googleapis-common-protos==1.61.0
+    # via google-api-core
 h11==0.14.0
     # via uvicorn
 h5py==3.10.0
@@ -229,6 +248,8 @@ ipython==8.16.1
     # via ipykernel
 isoduration==20.11.0
     # via jsonschema
+isort==5.12.0
+    # via efaar-benchmarking (pyproject.toml)
 itsdangerous==2.1.2
     # via starsessions
 jax==0.4.19
@@ -531,7 +552,10 @@ prometheus-client==0.17.1
 prompt-toolkit==3.0.39
     # via ipython
 protobuf==4.24.4
-    # via orbax-checkpoint
+    # via
+    #   google-api-core
+    #   googleapis-common-protos
+    #   orbax-checkpoint
 psutil==5.9.6
     # via
     #   ipykernel
@@ -639,6 +663,8 @@ requests==2.31.0
     # via
     #   fsspec
     #   gcsfs
+    #   google-api-core
+    #   google-cloud-storage
     #   jupyterlab-server
     #   lightning
     #   lightning-cloud
@@ -674,7 +700,7 @@ scanpy==1.9.5
     # via efaar-benchmarking (pyproject.toml)
 scikit-image==0.22.0
     # via efaar-benchmarking (pyproject.toml)
-scikit-learn==1.3.1
+scikit-learn==1.3.2
     # via
     #   efaar-benchmarking (pyproject.toml)
     #   pynndescent
@@ -759,6 +785,7 @@ tokenize-rt==5.2.0
     # via pyupgrade
 tomli==2.0.1
     # via
+    #   bandit
     #   black
     #   coverage
     #   jupyterlab
@@ -821,6 +848,8 @@ types-pkg-resources==0.1.3
     # via efaar-benchmarking (pyproject.toml)
 types-python-dateutil==2.8.19.14
     # via arrow
+types-setuptools==68.2.0.0
+    # via efaar-benchmarking (pyproject.toml)
 typing-extensions==4.8.0
     # via
     #   async-lru
@@ -840,8 +869,6 @@ typing-extensions==4.8.0
     #   uvicorn
 tzdata==2023.3
     # via pandas
-ujson==5.8.0
-    # via gcsfs
 umap-learn==0.5.4
     # via scanpy
 uri-template==1.3.0
@@ -858,7 +885,7 @@ uvicorn==0.23.2
     #   lightning-cloud
 validate-pyproject[all]==0.15
     # via efaar-benchmarking (pyproject.toml)
-virtualenv==20.24.5
+virtualenv==20.24.6
     # via
     #   pre-commit
     #   tox