scipion-em-xmipp 24.12.2__tar.gz → 25.6.1__tar.gz

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/CHANGELOG.md

@@ -1,7 +1,50 @@
-## Release 3.24.12.2 - Poseidon
-   - More scipion-em-xmipp
-      - Updating version for pypi requirements
-      - Bug cloning tag
+## Release 3.25.06.1 - Rhea
+- Disabling the default installation of dependencies to prevent breaking the scipion environment
+
+## Release 3.25.06.0 - Rhea
+- New protocols
+   - compute_likelihood: This protocol computes the likelihood of a set of particles with assigned angles when compared to a set of maps or atomic modelS
+
+- Protocols updated
+   - Max shift: tolerate movies without micrographs associated
+   - substract_projection: update command to boost and subtract to generate only one output stack
+   - Movie alignment consensus protocol: enables irregular input sets. Changes in functionality; comparisons between ons between shifts trajectories, and a additional change related to the minimum consensus or threshold for shifts correlation.
+   - volume_adjust_sub: better label for volume 1 vs 2
+   - convert_pdb: aDD binThreads
+   - align_volume: add possible
+   - particle_pick_consensus: Fixed ID mismatch when combining coordinate sets; now supports asymmetrical sets without indexing errors.
+   - movie_split_frames: now allows testing sum_frames, includes a summary, improved layout, and updated test.
+   - deep_Consensus: GPU handling
+   - Deep_hand: handling env to avoid system CUDA settings,  erasing cuda things from env['LD_LIBRARY_PATH']
+   - Extract particles protocol: force output boxsize
+   - reconstruct_fourier: correctEnvelope False by default
+   - reconstruct_highres: test updated, correctEnvelope False by default
+   - Structure map: Adding a dendrogram and removing some intermediate files
+
+
+- Protocols fixed
+   - simulate ctf: fix pre-CTF noise np.numpy, init generator for pre and post ctf noise
+   - validate FSCQ: test fixed
+   - resolution_monogenic_signal: fixing header in MonoRes
+   - protocol_process: CropResize halves fix
+   - Extract particles test fixed
+   - FSO viewer: the fso was failing when the fso did not cross some thresholds
+   - reconstruct_significant: fix gpu usage
+   - ransac: fix gpu usage
+     
+- Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols](https://i2pc.github.io/docs/Utils/Deprecated-programs/index.html)))
+   - XmippProtScreenDeepLearning
+
+- More scipion-em-xmipp
+   - Most of the Xmipp dependencies installed on Scipion env
+   - Updating version for pypi requirements
+   - Bug cloning tag
+   - Use toml for installation
+   - Bug fixed related to the WriteSetOfParticles and the Missing ExtraLabels (The Oier and Fede Adventures)
+   - Handling nvidia drivers error message
+   - improving deps installation
+   - Improved the help message of more than 60 protocols
+        
 ## Release 3.24.12 - Poseidon
    - New protocols
       - apply_tilt_to_ctf: Apply a local deviation to the CTF based on the micrograph's tilt

scipion_em_xmipp-25.6.1/PKG-INFO

@@ -0,0 +1,38 @@
+Metadata-Version: 2.1
+Name: scipion-em-xmipp
+Version: 25.6.1
+Summary: Plugin to use Xmipp programs within the Scipion framework.
+Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://github.com/I2PC/scipion-em-xmipp
+Project-URL: Issues, https://github.com/I2PC/scipion-em-xmipp/issues
+Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipion-pyworkflow>=3.0.31
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-image
+Requires-Dist: scipion-em
+Requires-Dist: scipion-app
+Requires-Dist: scipy<=1.10.0
+Requires-Dist: joblib
+Requires-Dist: peppercorn
+Requires-Dist: plotter
+Requires-Dist: PyWavelets
+
+[![Build](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml/badge.svg)](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml)
+
+# scipion-em-xmipp
+
+Plugin to use Xmipp programs within the Scipion framework.
+
+You can install it either, using the Scipion software following 
+the [Scipion's installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html)
+, (remember to install the scipion-em-xmipp plugin or remove the -noXmipp flag in the Scipion installation)**strongly recommended for non-developers** or cloning it on your own and 
+[linking it to Scipion](https://github.com/I2PC/xmipp#linking-standalone-version-to-scipion).
+The latter is only for those who intended to develop the Xmipp plugin.
+
+For **developers**, we strongly recommend to follow the guide on 
+[how to install xmipp-bundle](https://github.com/i2pc/xmipp#xmipp-as-a-standalone-bundle-for-developers) 
+in order to get a complet Xmipp's development ecosystem.

scipion_em_xmipp-25.6.1/pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scipion-em-xmipp"
+dynamic = ["version", "dependencies"]
+
+authors = [
+    {name = "Oier Lauzirika Zarrabeitia", email = "oierlauzi@bizkaia.eu"},
+    {name = "Alberto Garcia Mena", email = "alberto.garcia@cnb.csic.es"},
+    {name = "Carlos Oscar Sanchez Sorzano", email = "coss@cnb.csic.es"},
+]
+
+description = "Plugin to use Xmipp programs within the Scipion framework."
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = ["scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0"]
+license = {text = "GNU General Public License v3 (GPLv3)"}
+
+[project.urls]
+Homepage = "https://github.com/I2PC/scipion-em-xmipp"
+Issues = "https://github.com/I2PC/scipion-em-xmipp/issues"
+
+[tool.setuptools.dynamic]
+version = {attr = "xmipp3.version.__version__"}
+dependencies = {file = ["requirements.txt"]}
+
+[project.entry-points."pyworkflow.plugin"]
+xmipp3 = "xmipp3"
+
+[tool.setuptools.package-data]
+xmipp3 = ["protocols.conf", "xmipp_logo_devel.png"]

scipion_em_xmipp-25.6.1/scipion_em_xmipp.egg-info/PKG-INFO

@@ -0,0 +1,38 @@
+Metadata-Version: 2.1
+Name: scipion-em-xmipp
+Version: 25.6.1
+Summary: Plugin to use Xmipp programs within the Scipion framework.
+Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://github.com/I2PC/scipion-em-xmipp
+Project-URL: Issues, https://github.com/I2PC/scipion-em-xmipp/issues
+Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipion-pyworkflow>=3.0.31
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-image
+Requires-Dist: scipion-em
+Requires-Dist: scipion-app
+Requires-Dist: scipy<=1.10.0
+Requires-Dist: joblib
+Requires-Dist: peppercorn
+Requires-Dist: plotter
+Requires-Dist: PyWavelets
+
+[![Build](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml/badge.svg)](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml)
+
+# scipion-em-xmipp
+
+Plugin to use Xmipp programs within the Scipion framework.
+
+You can install it either, using the Scipion software following 
+the [Scipion's installation guide](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html)
+, (remember to install the scipion-em-xmipp plugin or remove the -noXmipp flag in the Scipion installation)**strongly recommended for non-developers** or cloning it on your own and 
+[linking it to Scipion](https://github.com/I2PC/xmipp#linking-standalone-version-to-scipion).
+The latter is only for those who intended to develop the Xmipp plugin.
+
+For **developers**, we strongly recommend to follow the guide on 
+[how to install xmipp-bundle](https://github.com/i2pc/xmipp#xmipp-as-a-standalone-bundle-for-developers) 
+in order to get a complet Xmipp's development ecosystem.

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -2,8 +2,8 @@ CHANGELOG.md
 LICENSE
 MANIFEST.in
 README.md
+pyproject.toml
 requirements.txt
-setup.py
 scipion_em_xmipp.egg-info/PKG-INFO
 scipion_em_xmipp.egg-info/SOURCES.txt
 scipion_em_xmipp.egg-info/dependency_links.txt
@@ -21,10 +21,53 @@ xmipp3/utils.py
 xmipp3/version.py
 xmipp3/wizards.py
 xmipp3/xmipp_logo.png
+xmipp3/xmipp_logo_devel.png
 xmipp3/convert/__init__.py
 xmipp3/convert/convert.py
 xmipp3/convert/dataimport.py
 xmipp3/convert/io_coordinates.py
+xmipp3/legacy/protocols/protocol_angular_resolution_alignment.py
+xmipp3/legacy/protocols/protocol_apply_deformation_zernike3d.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr_full.py
+xmipp3/legacy/protocols/protocol_classification_gpuCorr_semi.py
+xmipp3/legacy/protocols/protocol_classify_kmeans2d.py
+xmipp3/legacy/protocols/protocol_deep_align.py
+xmipp3/legacy/protocols/protocol_deep_denoising.py
+xmipp3/legacy/protocols/protocol_enrich.py
+xmipp3/legacy/protocols/protocol_kmeans_clustering.py
+xmipp3/legacy/protocols/protocol_metaprotocol_create_output.py
+xmipp3/legacy/protocols/protocol_metaprotocol_create_subset.py
+xmipp3/legacy/protocols/protocol_metaprotocol_discrete_heterogeneity_scheduler.py
+xmipp3/legacy/protocols/protocol_metaprotocol_golden_highres.py
+xmipp3/legacy/protocols/protocol_mltomo.py
+xmipp3/legacy/protocols/protocol_movie_average.py
+xmipp3/legacy/protocols/protocol_movie_opticalflow.py
+xmipp3/legacy/protocols/protocol_particle_boxsize.py
+xmipp3/legacy/protocols/protocol_reconstruct_heterogeneous.py
+xmipp3/legacy/protocols/protocol_rotational_spectra.py
+xmipp3/legacy/protocols/protocol_screen_deeplearning.py
+xmipp3/legacy/protocols/protocol_solid_angles.py
+xmipp3/legacy/protocols/protocol_split_volume.py
+xmipp3/legacy/protocols/protocol_split_volume_hierarchical_cluster.py
+xmipp3/legacy/protocols/protocol_subtract_projection.py
+xmipp3/legacy/tests/test_protocol_deep_denoising.py
+xmipp3/legacy/tests/test_protocols_angular_resolution_alignment.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_classifier.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_fullStreaming.py
+xmipp3/legacy/tests/test_protocols_gpuCorr_semiStreaming.py
+xmipp3/legacy/tests/test_protocols_metaprotocol_golden_highres.py
+xmipp3/legacy/tests/test_protocols_metaprotocol_heterogeneity.py
+xmipp3/legacy/tests/test_protocols_mixed_movies.py
+xmipp3/legacy/tests/test_protocols_solid_angles.py
+xmipp3/legacy/tests/test_protocols_subtract_projection.py
+xmipp3/legacy/tests/test_protocols_xmipp_movies.py
+xmipp3/legacy/viewers/viewer_angular_resolution_alignment.py
+xmipp3/legacy/viewers/viewer_deep_align.py
+xmipp3/legacy/viewers/viewer_metaprotocol_golden_highres.py
+xmipp3/legacy/viewers/viewer_mltomo.py
+xmipp3/legacy/viewers/viewer_solid_angles.py
+xmipp3/legacy/viewers/viewer_split_volume.py
 xmipp3/protocols/__init__.py
 xmipp3/protocols/protocol_align_volume.py
 xmipp3/protocols/protocol_align_volume_and_particles.py
@@ -45,6 +88,7 @@ xmipp3/protocols/protocol_classify_pca.py
 xmipp3/protocols/protocol_classify_pca_streaming.py
 xmipp3/protocols/protocol_compare_angles.py
 xmipp3/protocols/protocol_compare_reprojections.py
+xmipp3/protocols/protocol_compute_likelihood.py
 xmipp3/protocols/protocol_consensus_classes.py
 xmipp3/protocols/protocol_consensus_local_ctf.py
 xmipp3/protocols/protocol_convert_pdb.py
@@ -60,7 +104,6 @@ xmipp3/protocols/protocol_deep_hand.py
 xmipp3/protocols/protocol_deep_micrograph_screen.py
 xmipp3/protocols/protocol_denoise_particles.py
 xmipp3/protocols/protocol_eliminate_empty_images.py
-xmipp3/protocols/protocol_enrich.py
 xmipp3/protocols/protocol_extract_asymmetric_unit.py
 xmipp3/protocols/protocol_extract_particles.py
 xmipp3/protocols/protocol_extract_particles_movies.py
@@ -104,7 +147,6 @@ xmipp3/protocols/protocol_resolution_monogenic_signal.py
 xmipp3/protocols/protocol_rotate_volume.py
 xmipp3/protocols/protocol_rotational_symmetry.py
 xmipp3/protocols/protocol_screen_deepConsensus.py
-xmipp3/protocols/protocol_screen_deeplearning.py
 xmipp3/protocols/protocol_screen_particles.py
 xmipp3/protocols/protocol_shift_particles.py
 xmipp3/protocols/protocol_shift_volume.py
@@ -150,12 +192,14 @@ xmipp3/tests/test_protocol_compare_angles.py
 xmipp3/tests/test_protocol_consensus_classes3D.py
 xmipp3/tests/test_protocol_ctf_consensus.py
 xmipp3/tests/test_protocol_extract_asymmetric_unit.py
+xmipp3/tests/test_protocol_likelihood.py
 xmipp3/tests/test_protocol_monodir.py
 xmipp3/tests/test_protocol_multiple_fsc.py
 xmipp3/tests/test_protocol_multireference_alignability.py
 xmipp3/tests/test_protocol_reconstruct_fourier.py
 xmipp3/tests/test_protocol_screen_deepConsensus.py
 xmipp3/tests/test_protocol_simulate_ctf.py
+xmipp3/tests/test_protocol_split_frames.py
 xmipp3/tests/test_protocol_validate_fscq.py
 xmipp3/tests/test_protocol_validate_overfitting.py
 xmipp3/tests/test_protocols_add_noise.py
@@ -178,6 +222,7 @@ xmipp3/tests/test_protocols_zernike3d.py
 xmipp3/viewers/__init__.py
 xmipp3/viewers/plotter.py
 xmipp3/viewers/viewer.py
+xmipp3/viewers/viewer_LL_matrix.py
 xmipp3/viewers/viewer_analyze_local_ctf.py
 xmipp3/viewers/viewer_apply_tilt_to_ctf.py
 xmipp3/viewers/viewer_cl2d.py

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/scipion_em_xmipp.egg-info/entry_points.txt

@@ -1,3 +1,2 @@
 [pyworkflow.plugin]
 xmipp3 = xmipp3
-

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/xmipp3/__init__.py

@@ -27,13 +27,12 @@
 # **************************************************************************
 
 import json
+import re
 from datetime import datetime
 import pwem
 from pyworkflow import Config
 import pyworkflow.utils as pwutils
-from scipion.install.funcs import CommandDef
-from scipion import __version__ as scipionAppVersion
-from packaging.version import Version
+from scipion.install.funcs import CondaCommandDef
 from .base import *
 from .version import *
 from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL
@@ -152,21 +151,24 @@ class Plugin(pwem.Plugin):
         
         # When changing dependencies, increment _currentDepVersion
         CONDA_DEPENDENCIES = [
-            'cmake>=3.17',
-            'hdf5>=1.18',
-            'sqlite>=3',
-            'fftw>=3',
-            'mpich-mpicxx',
-            'c-compiler',
-            'cxx-compiler',
-            'make',
-            'openjdk',
-            'libtiff',
-            'libjpeg-turbo'
+	        "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
+            "hdf5>=1.18",
+            "sqlite>=3",
+            "fftw>=3",
+            "make",
+            "zlib",
+            "openjdk",
+            "libtiff",
+	    "libstdcxx-ng",
+            "libjpeg-turbo",
         ]
-        
-        if os.environ['CONDA_PREFIX'] is not None: # TODO replace with pyworkflow method when available.
-            commands = CommandDef('conda install -c conda-forge '  + ' '.join(CONDA_DEPENDENCIES))
+        if Config.isCondaInstallation():
+            condaEnvPath = os.environ['CONDA_PREFIX']
+            scipionEnv=os.path.basename(condaEnvPath)  # TODO: use pyworkflow method when released: Config.getEnvName()
+
+            commands = CondaCommandDef(scipionEnv, cls.getCondaActivationCmd())
+            commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
+            commands.touch("deps_installed.txt")
             env.addPackage(
                 'xmippDep', version=_currentDepVersion,
                 tar='void.tgz',
@@ -176,32 +178,41 @@ class Plugin(pwem.Plugin):
             )
         
         if develMode:
+            xmippSrc = 'xmippDev'
+            installCommands = [
+		        (f'cd {pwem.Config.EM_ROOT} && rm -rf {xmippSrc} && '
+		         f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+		         f'cd {xmippSrc} && '
+		         #f'git checkout {branchTest} && '
+		         f'./xmipp ', COMPILE_TARGETS)
+	        ]
+
             env.addPackage(
-                'xmippDev',
-                tar='void.tgz',
-                commands=[(f'cd {bundleDir} && ./xmipp', COMPILE_TARGETS)],
-                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
-                updateCuda=True,
-                default=False
-            )
-        
-        xmippSrc = f'xmippSrc-{version._binTagVersion}'
-        installCommands = [
-            (f'cd .. && rm -rf {xmippSrc} && '
-            f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
-            f'cd {xmippSrc} && '
-            f'git checkout {version._binTagVersion} && '
-            f'./xmipp --production True ', COMPILE_TARGETS)
-        ]
-        env.addPackage(
-            'xmippSrc', version=version._binTagVersion,
-            tar='void.tgz',
-            commands=installCommands,
-            neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
-            updateCuda=True,
-            default=not develMode
-        )
-        
+	            'xmippDev',
+	            tar='void.tgz',
+	            commands=installCommands,
+	            neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
+	            updateCuda=True,
+	            default=False
+	        )
+        else:
+            xmippSrc = f'xmippSrc-{version._binTagVersion}'
+            installCommands = [
+                (f'cd .. && rm -rf {xmippSrc} && '
+                f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+                f'cd {xmippSrc} && '
+                f'git checkout {version._binTagVersion} && '
+                f'./xmipp --production True ', COMPILE_TARGETS)
+            ]
+            env.addPackage(
+	                'xmippSrc', version=version._binTagVersion,
+	                tar='void.tgz',
+	                commands=installCommands,
+	                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
+	                updateCuda=True,
+	                default=not develMode
+	            )
+
         ## EXTRA PACKAGES ##
         installDeepLearningToolkit(cls, env)
 
@@ -216,45 +227,67 @@ class Plugin(pwem.Plugin):
                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
         
         return bundleDir if isBundle else None
-    
+
+def getNvidiaDriverVersion(plugin):
+    """Attempt to retrieve the NVIDIA driver version using different methods.
+    Only returns if a valid version string is found.
+    """
+    commands = [
+        ["nvidia-smi", "--query-gpu=driver_version", "--format=csv,noheader"],
+        ["cat", "/sys/module/nvidia/version"]
+    ]
+
+    for cmd in commands:
+        try:
+            output = subprocess.Popen(
+                cmd,
+                env=plugin.getEnviron(),
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE
+            ).communicate()[0].decode('utf-8').strip()
+
+            # Check if the output matches a version pattern like 530.30 or 470
+            match = re.match(r'^(\d+)', output)
+            if match:
+                return match.group(1)  # Return just the major version (e.g., "530")
+
+        except (ValueError, TypeError, FileNotFoundError, subprocess.SubprocessError):
+            continue  # Try next method
+
+    return None  # No valid version found
+
 def installDeepLearningToolkit(plugin, env):
 
     preMsgs = []
     cudaMsgs = []
     nvidiaDriverVer = None
     if os.environ.get('CUDA', 'True') == 'True':
-        try:
-            nvidiaDriverVer = subprocess.Popen(["nvidia-smi",
-                                                "--query-gpu=driver_version",
-                                                "--format=csv,noheader"],
-                                               env=plugin.getEnviron(),
-                                               stdout=subprocess.PIPE
-                                               ).stdout.read().decode('utf-8').split(".")[0]
-            if int(nvidiaDriverVer) < NVIDIA_DRIVERS_MINIMUM_VERSION:
-                preMsgs.append("Incompatible driver %s" % nvidiaDriverVer)
-                cudaMsgs.append(f"Your NVIDIA drivers are too old (<{NVIDIA_DRIVERS_MINIMUM_VERSION}). "
-                                "Tensorflow was installed without GPU support. "
-                                "Just CPU computations enabled (slow computations)."
-                                f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
-                                "set CUDA=True in 'scipion.conf' file")
-                nvidiaDriverVer = None
-        except (ValueError, TypeError, FileNotFoundError):
-            nvidiaDriverVer = None
-            preMsgs.append("Not nvidia driver found. Type: "
-                           " nvidia-smi --query-gpu=driver_version --format=csv,noheader")
-            preMsgs.append(
-                "CUDA will NOT be USED. (not found or incompatible)")
-            msg = ("Tensorflow installed without GPU. Just CPU computations "
-                   "enabled (slow computations).")
-            cudaMsgs.append(msg)
-            useGpu = False
+        nvidiaDriverVer = getNvidiaDriverVersion(plugin)
 
-    if nvidiaDriverVer is not None:
-        preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)
-        msg = "Tensorflow will be installed with CUDA SUPPORT."
+    if nvidiaDriverVer is None:
+        preMsgs.append("Not nvidia driver found. Type: "
+                       " nvidia-smi --query-gpu=driver_version --format=csv,noheader")
+        preMsgs.append(
+            "CUDA will NOT be USED. (not found or incompatible)")
+        msg = ("Tensorflow installed without GPU. Just CPU computations "
+               "enabled (slow computations).")
         cudaMsgs.append(msg)
-        useGpu = True
+        useGpu = False
 
+    else:
+        if int(nvidiaDriverVer) < NVIDIA_DRIVERS_MINIMUM_VERSION:
+            preMsgs.append("Incompatible driver %s" % nvidiaDriverVer)
+            cudaMsgs.append(f"Your NVIDIA drivers are too old (<{NVIDIA_DRIVERS_MINIMUM_VERSION}). "
+                            "Tensorflow was installed without GPU support. "
+                            "Just CPU computations enabled (slow computations)."
+                            f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
+                            "set CUDA=True in 'scipion.conf' file")
+            useGpu = False
+        else:
+            preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)
+            msg = "Tensorflow will be installed with CUDA SUPPORT."
+            cudaMsgs.append(msg)
+            useGpu = True
 
     # commands  = [(command, target), (cmd, tgt), ...]
     cmdsInstall = list(CondaEnvManager.yieldInstallAllCmds(useGpu=useGpu))

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/xmipp3/base.py

@@ -155,9 +155,10 @@ class XmippProtocol:
         # Looking for the installation target for that conda environment.
         kerasError = False
         envName = CondaEnvManager.getCondaName(self, **kwargs)
+        targetName = CondaEnvManager.getCondaEnvTargetFilename(self, envName)
         if not os.path.isfile(os.path.join(pwem.Config.EM_ROOT,
                                            XMIPP_DLTK_NAME,
-                                           envName+'.yml')):
+                                           targetName)):
             errors.append("*%s environment not found*. "
                           "Required to run this protocol." % envName)
             kerasError = True

{scipion-em-xmipp-24.12.2 → scipion_em_xmipp-25.6.1}/xmipp3/convert/convert.py

@@ -477,7 +477,7 @@ def imageToRow(img, imgRow, imgLabel, **kwargs):
         acquisitionToRow(img.getAcquisition(), imgRow)
 
     # Write all extra labels to the row
-    objectToRow(img, imgRow, {}, extraLabels=IMAGE_EXTRA_LABELS)
+    objectToRow(img, imgRow, {}, extraLabels=IMAGE_EXTRA_LABELS + kwargs.get('extraLabels', []))
 
     # Provide a hook to be used if something is needed to be
     # done for special cases before converting image to row