Merge pull request #1027 from I2PC/release-3.25.06

Release 3.25.06

Author: albertmena

CHANGELOG.md

@@ -23,7 +23,7 @@
    - Enhanced data collection steps (context suggests improvements in reproducibility or logging)
 
    ### More Xmipp  
-   - DLTK environments: channels limited to conda-forge and pip. Updated deepEMhancer version and models
+   - DLTK environments: channels limited to conda-forge and pip. Updated deepEMhancer version and models, update all enviroments
    - Allowing to skip sorting in metadata_vec::split
 
 ## Release 3.24.12.0 - Poseidon
@@ -35,7 +35,7 @@
         - angular_continuous_assign2_gpu: Make a continuous angular assignment with GPU
         - cuda_fourier_projection
         - predict_deep_center
-        - cl2d_clustering.py
+        - cl2d_clustering
 
    - Programs updated
       - tomogram_reconstruction:  averaging with gold standard, tigre with internal interpolation, enviroment of tigre updated

README.md

@@ -20,9 +20,7 @@ For developers, it becomes handy to install Xmipp in an external directory for e
 
 The first step is to download Xmipp sources:
 
-`git clone https://github.com/I2PC/xmipp.git`
-
-`cd xmipp`
+`git clone https://github.com/I2PC/xmipp.git xmipp-bundle & cd xmipp-bundle`
 
 If you want to checkout an scpecific branch use the following command. For repositories where the branch does not exist, devel is utilized.
 

src/xmipp/bindings/python/envs_DLTK/xmipp_DLTK_v0.3-gpu.yml

@@ -9,6 +9,8 @@ channels:
 dependencies:
   - python=3.7
   - libstdcxx-ng # To be compatible with scipion env
+  - cudnn=7.6
+  - cudatoolkit==10.0.130
   - pip
   - pip:
       - tensorflow-gpu==1.15.0

src/xmipp/bindings/python/envs_DLTK/xmipp_deepEMhancer.yml

@@ -6,7 +6,7 @@ channels:
   - rsanchez1369
 dependencies:
   - python=3.10
-  - deepemhancer=0.16 #CUDA > 10 required. Drivers nvidia >= 450.80.02
+  - deepemhancer>=0.16 #CUDA > 10 required. Drivers nvidia >= 450.80.02
   - numba
   - h5py
   - libstdcxx-ng # To be compatible with scipion env

src/xmipp/bindings/python/xmipp_base.py

@@ -255,6 +255,16 @@ def getCondaEnv(env, condaEnv):
         env['PYTHONWARNINGS'] = 'ignore::FutureWarning'  # to skip warnings
         return env
 
+    def getCondaEnvTargetFilename(self, name):
+        env = CondaEnvManager.XMIPP_CONDA_ENVS[name]
+
+        if "versionId" in env:
+            target = f'{name}-{env["versionId"]}.yml'
+        else:
+            target = f'{name}.yml'
+
+        return target
+
     @staticmethod
     def getCondaActivationCmd():
         """ This method takes the command to activate conda