Revision v2

.gitignore

@@ -5,3 +5,4 @@ notebooks/.ipynb_checkpoints
 .DS_Store
 .ipynb_checkpoints
 /notebooks/eval/cleaned/tests/data
+/tmp/

envs/csi_pip_req_minimal.txt

@@ -0,0 +1,32 @@
+# Do not forget to install csi package (current) after installing the following
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+#scib-metrics==0.5.1
+scib-metrics==0.3.3
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+leidenalg==0.10.2
+jax==0.4.10
+jaxlib==0.4.10
+ml-dtypes==0.1.0
+harmonypy==0.0.10
+

envs/perturb_pip_req_minimal.txt

@@ -0,0 +1,28 @@
+scgen==2.1.0
+
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+scib-metrics==0.5.1
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+
+

envs/pipelines_pip_req_minimal.txt

@@ -0,0 +1,5 @@
+pandas==1.5.3
+wandb==0.17.5
+seml=0.3.7
+numpy==1.24.3
+

envs/r_env_readme.txt

@@ -0,0 +1,21 @@
+# We used apptainer based on ml-verse
+```
+apptainer build --sandbox my_ml_verse docker://rocker/ml-verse
+```
+
+
+# Install python pacjages
+```
+pip install anndata
+```
+
+# Install R packages inside R:
+
+```
+install.packages("argparse")
+install.packages("Seurat")
+install.packages("harmony")
+install.packages("anndata")
+install.packages("reticulate")
+```
+

envs/scglue_pip_req_minimal.txt

@@ -0,0 +1,28 @@
+scglue==0.3.2
+
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+scib-metrics==0.5.1
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+
+

envs/scmgca_pip_req_freeze.txt

@@ -0,0 +1,104 @@
+absl-py==0.15.0
+# anndata==0.9.2
+astunparse==1.6.3
+backcall==0.2.0
+cached-property==1.5.2
+cachetools==4.2.4
+certifi==2021.10.8
+charset-normalizer==2.0.12
+cloudpickle==1.3.0
+cycler==0.11.0
+#dataclasses==0.8
+decorator==4.4.2
+dm-tree==0.1.7
+flatbuffers==1.12
+future==0.18.2
+gast==0.3.3
+get_version==2.1
+google-auth==1.28.0
+google-auth-oauthlib==0.4.4
+google-pasta==0.2.0
+grpcio==1.34.1
+# h5py==3.11.0
+hyperopt==0.2.5
+idna==3.3
+igraph==0.9.11
+importlib-metadata==4.8.3
+ipython==7.16.3
+ipython-genutils==0.2.0
+jedi==0.17.2
+jgraph==0.2.1
+joblib==1.1.0
+keras-nightly==2.5.0.dev2021032900
+Keras-Preprocessing==1.1.2
+kiwisolver==1.3.1
+legacy-api-wrap==1.2
+leidenalg==0.8.8
+llvmlite==0.34.0
+lxml==4.8.0
+Markdown==3.3.6
+matplotlib==3.3.4
+natsort==8.1.0
+networkx==2.5.1
+numba==0.51.2
+numexpr==2.7.3
+numpy==1.18.1
+oauthlib==3.1.0
+opt-einsum==3.3.0
+packaging==21.3
+pandas==1.1.5
+parso==0.7.1
+patsy==0.5.1
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==8.4.0
+prompt-toolkit==3.0.29
+protobuf==3.19.4
+ptyprocess==0.7.0
+py4j==0.10.9.7
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+Pygments==2.12.0
+pynndescent==0.5.6
+pyparsing==3.0.8
+python-dateutil==2.8.2
+python-igraph==0.9.11
+pytz==2022.1
+requests==2.27.1
+requests-oauthlib==1.3.1
+rsa==4.8
+scanpy==1.6.0
+scikit-learn==0.24.2
+scipy==1.4.1
+seaborn==0.11.1
+setuptools-scm==6.4.2
+sinfo==0.3.4
+six==1.15.0
+spektral==0.6.1
+statsmodels==0.12.2
+stdlib-list==0.8.0
+tables==3.6.1
+tensorboard==2.4.1
+tensorboard-plugin-wit==1.8.0
+tensorflow==2.3.0
+tensorflow-estimator==2.3.0
+tensorflow-gpu==2.3.0
+tensorflow-probability==0.11.0
+termcolor==1.1.0
+texttable==1.6.4
+threadpoolctl==3.1.0
+tomli==1.2.3
+tqdm==4.41.1
+traitlets==4.3.3
+typing-extensions==3.7.4.3
+umap-learn==0.4.2
+urllib3==1.26.9
+wcwidth==0.2.5
+Werkzeug==2.0.3
+wrapt==1.12.1
+xlrd==1.2.0
+zipp==3.6.0
+
+seml
+#scib-metrics==0.5.1
+scMGCA==1.0.7

envs/sysvi_pip_req_minimal.txt

@@ -0,0 +1,30 @@
+anndata==0.11.1
+colorcet==3.1.0
+joblib==1.4.2
+matplotlib==3.9.3
+networkx==3.4.2
+numpy==1.26.4
+pandas==2.2.3
+#rpy2
+sacred==0.8.7
+scanpy==1.10.4
+scipy==1.14.1
+seaborn==0.13.2
+seml==0.5.4
+statsmodels==0.14.4
+torch==2.5.1
+torchmetrics==1.6.0
+typing_extensions==4.12.2
+adjustText==1.3.0
+# pytorch_lightning
+#scib-metrics
+#scib-metrics
+scib-metrics==0.5.1
+# scvi-tools
+
+# git+https://github.com/Hrovatin/scvi-tools.git@main
+git+https://github.com/Hrovatin/scvi-tools.git@stable
+
+scikit-learn==1.6.0
+leidenalg==0.10.2
+

envs/update_requirements.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+# Check if the requirements file is provided
+if [ -z "$1" ]; then
+  echo "Usage: $0 <path_to_requirements.txt>"
+  exit 1
+fi
+
+REQUIREMENTS_FILE=$1
+
+# Check if the file exists
+if [ ! -f "$REQUIREMENTS_FILE" ]; then
+  echo "Error: File $REQUIREMENTS_FILE does not exist."
+  exit 1
+fi
+
+# Create a temporary file to store updated requirements
+UPDATED_FILE=$(mktemp)
+
+# Get the list of installed packages with versions
+PIP_FREEZE=$(pip freeze)
+
+# Process each line in the requirements file
+while read -r PACKAGE; do
+  if [[ -z "$PACKAGE" || "$PACKAGE" == \#* ]]; then
+    # Keep comments and empty lines unchanged
+    echo "$PACKAGE" >> "$UPDATED_FILE"
+  else
+    # Extract the package version from pip freeze
+    VERSION=$(echo "$PIP_FREEZE" | grep "^${PACKAGE}==" || true)
+    if [ -n "$VERSION" ]; then
+      echo "$VERSION" >> "$UPDATED_FILE"
+    else
+      echo "# $PACKAGE (not found)" >> "$UPDATED_FILE"
+    fi
+  fi
+done < "$REQUIREMENTS_FILE"
+
+# Overwrite the original file with the updated content
+mv "$UPDATED_FILE" "$REQUIREMENTS_FILE"
+
+echo "Updated $REQUIREMENTS_FILE with versions from pip freeze."
+
+