Merge branch '277-new-tomodrgn-module' into 'master'

Resolve "new tomodrgn module"

Closes #277

See merge request Pmodules/buildblocks!439

EM/tomodrgn/README.md

@@ -0,0 +1,13 @@
+ Installation remarks for Tomodrgn: 
+
+1.) function in tomodrgn/analysis.py is not valid with matplotlib v3.8 anymore, this is why the function is substituted in the build script:
+sed -i 's/cbar.draw_all/cbar._draw_all/' tomodrgn/analysis.py 
+
+2.) the tomodrgn quicktest script can be exectued by : 
+python /opt/psi/EM/tomodrgn/0.2.2/tomodrgn/testing/quicktest.py
+REMARK: This file was changed in order to provide the argument --datadir /opt/psi/EM/tomodrgn/0.2.2/tomodrgn/testing/, otherwise it will look for the "data" folder in the current working dir. 
+
+3.) quicktest is run without the two arguments: --num-workers (dafault =0) and --prefetch-factor (default should be None, but is actually 2), which throws an error,was fixed by changing the default of --prefetch-factor to None in the file /opt/psi/EM/tomodrgn/0.2.2/miniconda/envs/tomodrgn_0.2.2/lib/python3.9/site-packages/tomodrgn/commands/train_vae.py   
+
+
+

EM/tomodrgn/build

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+#!/usr/bin/env modbuild
+
+
+pbuild::configure() {
+    #MINICONDA INSTALL
+    mkdir -p  "$PREFIX/miniconda"
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O "$PREFIX/miniconda/miniconda.sh"
+    bash "$PREFIX/miniconda/miniconda.sh" -b -u -p "$PREFIX/miniconda/"
+
+ 
+    #CREATE ENV , make sure to source the "correct" conda.sh
+    "$PREFIX/miniconda/condabin/conda" env create --name "tomodrgn_$V" -f "$BUILDBLOCK_DIR/environment.yaml"
+    source "$PREFIX/miniconda/etc/profile.d/conda.sh"
+    conda activate "tomodrgn_$V"
+
+    #CP SOURCE CODE
+    mkdir "$PREFIX/tomodrgn"
+    cd "$PREFIX/tomodrgn"
+    cp -r "$SRC_DIR"/* .
+    #FIX MATPLOTLIB VERSION issue
+    sed -i 's/cbar.draw_all/cbar._draw_all/' tomodrgn/analysis.py
+    #INSTALL IN ENV
+    pip install . 
+
+}
+
+#DO NOTHING
+pbuild::compile(){
+    :
+}
+
+pbuild::install(){
+    :
+}

EM/tomodrgn/environment.yaml

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+channels:
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - pytorch-gpu>=1.11.0
+  - cudatoolkit>=11.0
+  - pandas
+  - seaborn
+  - scikit-learn
+  - umap-learn
+  - ipython_genutils
+  - notebook
+  - pip
+  - pip:
+    - ipyvolume>=0.6.0
+    - pythreejs>=2.4.2
+

EM/tomodrgn/files/config.yaml

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+format: 1
+tomodrgn:
+  deaults:
+    group: EM
+    overlay: base
+    relstage: unstable
+    urls:
+      - url: https://github.com/bpowell122/tomodrgn/archive/refs/tags/v${V_PKG}.tar.gz
+        name: tomodrgn-${V_PKG}.tar.gz
+  versions:
+    0.2.2:

EM/tomodrgn/modulefile

@@ -0,0 +1,34 @@
+#%Module1.0
+
+module-whatis           "TomoDRGN - analyzing structural heterogeneity in cryo-electron sub-tomograms"
+module-url              "https://github.com/bpowell122/tomodrgn"
+module-license          "-"
+module-maintainer       "Greta Assmann <greta.assmann@psi.ch>"
+
+module-help     "https://github.com/bpowell122/tomodrgn"
+
+
+# Check for supported shell types
+set shelltype [module-info shelltype]
+switch -- $shelltype {
+    "sh" {
+        puts stdout "source \"\${PREFIX}\"/miniconda/etc/profile.d/conda.sh;\n"
+    }
+    default {
+        puts stderr "Shells of type '$shelltype' are NOT supported!"
+    }
+}
+
+
+switch [module-info mode] {
+    "load" {
+      # Relies on the anaconda module being loaded since we need to update the path
+      puts stdout "conda activate $P_$V;\n"
+    }
+    "unload" -
+    "remove" {
+        puts stdout "conda deactivate;\n"
+    }
+}
+
+