Merge pull request #11 from scipion-em/devel

release 3.1

.gitignore

@@ -1,8 +1,16 @@
-# Python compilation files
-*.pyc
-
-# Ignore temporary packaging folder
-*.egg-info
-
-# IDE files
+#### Eclipse and so on
+.project
+.cproject
+.pydevproject
+.classpath
 .idea
+
+#### Python
+build/
+dist/
+*.egg-info/
+*.egg
+*.py[cod]
+__pycache__/
+*.so
+*~

CHANGES.txt

@@ -1,3 +1,5 @@
-3.0.1
------
-  - Installation does not fail but is never complete. So installb modelangelo will git pull all the time.
+3.1:
+ - update installation
+ - create constants
+ - add MODEL_ANGELO_CUDA_LIB
+3.0.1: Installation does not fail but is never complete. So installb modelangelo will git pull all the time.

MANIFEST.in

@@ -1,3 +1,5 @@
 include *.txt
 include *.rst
-include LICENSE
+include LICENSE
+include modelangelo/protocols.conf
+include modelangelo/logo.jpeg

README.rst

@@ -54,7 +54,7 @@ conda activate will not be prepended. For example (loading model-angelo as a mod
 
     MODEL_ANGELO_ACTIVATION = module load model-angelo/main
 
-
+If you need to use CUDA different from the one used during Scipion installation (defined by *CUDA_LIB*), you can add *MODEL_ANGELO_CUDA_LIB* variable to the config file.
 
 Protocols
 ---------

modelangelo/__init__.py

@@ -6,7 +6,7 @@
 # *
 # * This program is free software; you can redistribute it and/or modify
 # * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 2 of the License, or
+# * the Free Software Foundation; either version 3 of the License, or
 # * (at your option) any later version.
 # *
 # * This program is distributed in the hope that it will be useful,
@@ -23,29 +23,18 @@
 # *  e-mail address '[email protected]'
 # *
 # **************************************************************************
-import datetime
+from datetime import datetime as dt
 import os
 
 import pwem
-import pyworkflow
-from pyworkflow.utils import runJob
+import pyworkflow.utils as pwutils
 from scipion.install.funcs import VOID_TGZ
 
-__version__ = "3.0.3"
-_logo = "icon.jpeg"
-_references = ['mabioarxive']
+from .constants import *
 
-# TODO: move to constants
-MA_VERSION = 'git'
-# Use this variable to activate an environment from the Scipion conda
-MODEL_ANGELO_ENV_ACTIVATION_VAR = "MODEL_ANGELO_ENV_ACTIVATION"
-# Use this general activation variable when installed outside Scipion
-MODEL_ANGELO_ACTIVATION_VAR = "MODEL_ANGELO_ACTIVATION"
-
-# models
-MODELS_VERSION = '0.1'
-MODELS_PKG_NAME = 'modelangelomodels'
-TORCH_HOME_VAR = 'TORCH_HOME'
+__version__ = "3.1"
+_logo = "logo.jpeg"
+_references = ['jamali2023']
 
 
 class Plugin(pwem.Plugin):
@@ -55,9 +44,10 @@ def _defineVariables(cls):
         cls._defineVar(MODEL_ANGELO_ACTIVATION_VAR, '')
         cls._defineVar(MODEL_ANGELO_ENV_ACTIVATION_VAR, cls.getActivationCmd(MA_VERSION))
         cls._defineEmVar(TORCH_HOME_VAR, MODELS_PKG_NAME + "-" + MODELS_VERSION)
+        cls._defineVar(MODEL_ANGELO_CUDA_LIB, pwem.Config.CUDA_LIB)
 
     @classmethod
-    def getModelAngeloCmd(cls, *args):
+    def getModelAngeloCmd(cls):
         cmd = cls.getVar(MODEL_ANGELO_ACTIVATION_VAR)
         if not cmd:
             cmd = cls.getCondaActivationCmd()
@@ -67,11 +57,15 @@ def getModelAngeloCmd(cls, *args):
 
     @classmethod
     def getEnviron(cls):
-        environ = pyworkflow.utils.Environ(os.environ)
+        environ = pwutils.Environ(os.environ)
         torch_home = cls.getVar(TORCH_HOME_VAR)
-        # For GPU, we need to add to LD_LIBRARY_PATH the path to Cuda/lib
         environ.set(TORCH_HOME_VAR, torch_home)
+
+        cudaLib = cls.getVar(MODEL_ANGELO_CUDA_LIB)
+        environ.addLibrary(cudaLib)
+
         return environ
+
     @classmethod
     def getActivationCmd(cls, version):
         return'conda activate modelangelo-' + version
@@ -80,14 +74,13 @@ def getActivationCmd(cls, version):
     def defineBinaries(cls, env):
 
         def defineModelAngeloInstallation(version):
+            installed = "last-pull-%s.txt" % dt.now().strftime("%y%h%d-%H%M%S")
 
-            installed = "last-pull-%s.txt" % datetime.datetime.now().strftime("%y%h%d-%H%M%S")
-
-            # For modelangelo
-            modelangelo_commands = []
-            modelangelo_commands.append(('git clone https://github.com/3dem/model-angelo.git', 'model-angelo'))
-            modelangelo_commands.append((getCondaInstallation(version), 'env-created.txt'))
-            modelangelo_commands.append(('cd model-angelo && git pull && touch ../%s' % installed, installed))
+            modelangelo_commands = [
+                ('git clone https://github.com/3dem/model-angelo.git', 'model-angelo'),
+                (getCondaInstallation(version), 'env-created.txt'),
+                ('cd model-angelo && git pull && touch ../%s' % installed, installed)
+            ]
 
             env.addPackage('modelangelo', version=version,
                            commands=modelangelo_commands,
@@ -96,31 +89,26 @@ def defineModelAngeloInstallation(version):
 
         def getCondaInstallation(version):
             installationCmd = cls.getCondaActivationCmd()
-            installationCmd += 'conda create -y -n modelangelo-' + version + ' python=3.9 && '
+            installationCmd += 'conda create -y -n modelangelo-' + version + ' python=3.10 && '
             installationCmd += cls.getActivationCmd(version) + ' && '
-            installationCmd += 'cd model-angelo && python -m pip install -r requirements.txt && '
-            installationCmd += 'conda install -y pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch && '
-            installationCmd += 'python -m pip install -e . && '
+            installationCmd += 'conda install -y pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia && '
+            installationCmd += 'cd model-angelo && pip install -r requirements.txt && '
+            installationCmd += 'pip install -e . && '
             installationCmd += 'touch ../env-created.txt'
 
             return installationCmd
 
-        # Define model angelo installations
         defineModelAngeloInstallation(MA_VERSION)
 
         # Models download
         installationCmd = ""
         installationCmd += 'export TORCH_HOME=$PWD && '
-        installationCmd += cls.getCondaActivationCmd() + " " +  cls.getActivationCmd(MA_VERSION) + ' && '
+        installationCmd += cls.getCondaActivationCmd() + " " + cls.getActivationCmd(MA_VERSION) + ' && '
         installationCmd += 'python -m model_angelo.utils.setup_weights --bundle-name original && '
         installationCmd += 'python -m model_angelo.utils.setup_weights --bundle-name original_no_seq'
 
-
-        env.addPackage('modelangelomodels', version="0.1",
-                       commands=[(installationCmd,["hub/checkpoints/model_angelo/original_no_seq/success.txt",
-                                                   "hub/checkpoints/model_angelo/original/success.txt"])],
+        env.addPackage('modelangelomodels', version=MODELS_VERSION,
+                       commands=[(installationCmd, [f"hub/checkpoints/model_angelo_v{MODELS_VERSION}/original_no_seq/success.txt",
+                                                    f"hub/checkpoints/model_angelo_v{MODELS_VERSION}/original/success.txt"])],
                        tar=VOID_TGZ,
                        default=True)
-
-
-

modelangelo/bibtex.py

@@ -7,7 +7,7 @@
 # *
 # * This program is free software; you can redistribute it and/or modify
 # * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 2 of the License, or
+# * the Free Software Foundation; either version 3 of the License, or
 # * (at your option) any later version.
 # *
 # * This program is distributed in the hope that it will be useful,
@@ -26,15 +26,14 @@
 # **************************************************************************
 
 """
-@article{mabioarxive,
-  doi = "https://doi.org/10.48550/arxiv.2210.00006",
-  url = "https://arxiv.org/abs/2210.00006",
-  author = "Jamali, Kiarash and Kimanius, Dari and Scheres, Sjors",
-  keywords = "Quantitative Methods (q-bio.QM), Artificial Intelligence (cs.AI), Machine Learning (cs.LG), Biomolecules (q-bio.BM), FOS: Biological sciences, FOS: Biological sciences, FOS: Computer and information sciences, FOS: Computer and information sciences",
-  title = "ModelAngelo: Automated Model Building in Cryo-EM Maps",
-  publisher = "arXiv",
-  year = "2022",
-  copyright = "Creative Commons Attribution 4.0 International"
+@article{jamali2023,
+author = {Kiarash Jamali and Lukas Kall and Rui Zhang and Alan Brown and Dari Kimanius and Sjors Scheres},
+title = {Automated model building and protein identification in cryo-EM maps},
+year = {2023},
+doi = {https://dx.doi.org/10.1101/2023.05.16.541002},
+publisher = {Cold Spring Harbor Laboratory},
+URL = {https://www.biorxiv.org/content/early/2023/05/16/2023.05.16.541002},
+journal = {bioRxiv}
 }
 
 """

modelangelo/wizards/__init__.py → modelangelo/constants.py

@@ -1,12 +1,12 @@
-# -*- coding: utf-8 -*-
 # **************************************************************************
 # *
-# * Authors:     Roberto Marabini
+# * Authors:     Grigory Sharov ([email protected])
 # *
+# * MRC Laboratory of Molecular Biology (MRC-LMB)
 # *
 # * This program is free software; you can redistribute it and/or modify
 # * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 2 of the License, or
+# * the Free Software Foundation; either version 3 of the License, or
 # * (at your option) any later version.
 # *
 # * This program is distributed in the hope that it will be useful,
@@ -23,3 +23,15 @@
 # *  e-mail address '[email protected]'
 # *
 # **************************************************************************
+
+MA_VERSION = 'git'
+# Use this variable to activate an environment from the Scipion conda
+MODEL_ANGELO_ENV_ACTIVATION_VAR = "MODEL_ANGELO_ENV_ACTIVATION"
+# Use this general activation variable when installed outside Scipion
+MODEL_ANGELO_ACTIVATION_VAR = "MODEL_ANGELO_ACTIVATION"
+MODEL_ANGELO_CUDA_LIB = "MODEL_ANGELO_CUDA_LIB"
+
+# models
+MODELS_VERSION = '1.0'
+MODELS_PKG_NAME = 'modelangelomodels'
+TORCH_HOME_VAR = 'TORCH_HOME'

modelangelo/protocols/__init__.py

@@ -1,6 +1,24 @@
-# -*- coding: utf-8 -*-
-# **************************************************************************
-# Module to declare protocols
-# Find documentation here: https://scipion-em.github.io/docs/docs/developer/creating-a-protocol
-# **************************************************************************
-from .protocol_model_angelo import ProtModelAngelo
+# ***************************************************************************
+# * Authors:   Roberto Marabini ([email protected])
+# *
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address '[email protected]'
+# ***************************************************************************
+
+from .protocol_model_angelo import ProtModelAngelo