Simplify installation instructions

.github/workflows/github_actions.yml

@@ -36,17 +36,15 @@ jobs:
           echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
       - if: matrix.install-type == 'user'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif
+          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
-          conda install -c bioconda hmmer hhsuite
           pip install alphapulldown==2.0.0b6
       - if: matrix.install-type == 'developer'
         run: |
-          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 modelcif
+          conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 hmmer hhsuite modelcif
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
-          conda install -c bioconda hmmer hhsuite
           pip install -e .
           pip install -e ColabFold --no-deps
           pip install -e alphafold --no-deps
@@ -60,10 +58,10 @@ jobs:
           # python setup.py install --disable-cuda-ext
           # cd .
           python test/test_python_imports.py
-      - if: matrix.install-type == 'developer'
-        run: |
-          eval "$(conda shell.bash hook)"
-          conda activate AlphaPulldown
+      #- if: matrix.install-type == 'developer'
+      #  run: |
+      #    eval "$(conda shell.bash hook)"
+      #    conda activate AlphaPulldown
           pytest -s test/test_custom_db.py
           pytest -s test/test_remove_clashes_low_plddt.py
           pytest -s test/test_modelcif.py

README.md

@@ -426,17 +426,16 @@ AlphaPulldown can be used as a set of scripts for every particular step.
 
 ### 0.1. Create Anaconda environment
 
-**Firstly**, install [Anaconda](https://www.anaconda.com/) and create an AlphaPulldown environment, gathering necessary dependencies:
+**Firstly**, install [Anaconda](https://www.anaconda.com/) and create an AlphaPulldown environment, gathering necessary dependencies. We recommend to use mamba to speed up solving of dependencies:
 
 ```bash
-conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.10 openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata hhsuite modelcif
+conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==3.11 openmm==8.0 pdbfixer==1.9 kalign2 hhsuite hmmer modelcif
 ```
        
 **Optionally**, if you do not have it yet on your system, install [HMMER](http://hmmer.org/documentation.html) from Anaconda:
 
 ```bash
 source activate AlphaPulldown
-conda install -c bioconda hmmer
 ```
 This usually works, but on some compute systems, users may prefer to use other versions or optimized builds of HMMER and HH-suite that are already installed.
 
@@ -524,7 +523,7 @@ Please [add your SSH key to your GitHub account](https://docs.github.com/en/auth
     ```bash
     source activate AlphaPulldown
     cd AlphaPulldown
-    pip install alphapulldown
+    pip install .
     pip install -e . --no-deps
     pip install -e ColabFold --no-deps
     pip install -e alphafold --no-deps

setup.cfg

@@ -58,7 +58,6 @@ install_requires =
     h5py>=3.1.0
     matplotlib>=3.3.3
     ml-collections>=0.1.0
-    numpy
     pandas>=1.5.3
     importlib-resources>=6.1.0
     biopython>=1.82
@@ -72,6 +71,10 @@ install_requires =
     jupyterlab>=3.0
     ipywidgets
     pytest>=6.0
+    importlib-metadata>=4.8.2,<5.0.0
+    tensorflow-cpu>=2.16.1
+    chex>=0.1.86
+    immutabledict>=2.0.0
 scripts = ./alphafold/run_alphafold.py 
           ./alphapulldown/scripts/create_individual_features.py 
           ./alphapulldown/scripts/run_multimer_jobs.py

test/check_predict_structure.py

@@ -14,7 +14,7 @@
 import os
 import subprocess
 import json
-from alphapulldown.utils.calculate_rmsd import calculate_rmsd_and_superpose
+#from alphapulldown.utils.calculate_rmsd import calculate_rmsd_and_superpose
 import alphapulldown
 from absl.testing import absltest
 from absl.testing import parameterized
@@ -301,7 +301,7 @@ def testRunWithTemplate(self):
             target = os.path.join(self.output_dir, "3L4Q_A_and_3L4Q_C", f"ranked_{i}.pdb")
             assert os.path.exists(target)
             with tempfile.TemporaryDirectory() as temp_dir:
-                rmsds = calculate_rmsd_and_superpose(reference, target, temp_dir=temp_dir)
+                #rmsds = calculate_rmsd_and_superpose(reference, target, temp_dir=temp_dir)
                 print(f"Model {i} RMSD {rmsds}")
         # Best RMSD is high because of FAST=True
         # TODO: assert min(rmsd_chain_b) < ??