scipion-em-xmipp 24.6.0.0__tar.gz → 24.12.2__tar.gz

scipion-em-xmipp-24.6.0.0/CHANGES.md → scipion-em-xmipp-24.12.2/CHANGELOG.md

@@ -1,3 +1,45 @@
+## Release 3.24.12.2 - Poseidon
+   - More scipion-em-xmipp
+      - Updating version for pypi requirements
+      - Bug cloning tag
+## Release 3.24.12 - Poseidon
+   - New protocols
+      - apply_tilt_to_ctf: Apply a local deviation to the CTF based on the micrograph's tilt
+    angle
+      - mics_defocus_balancer: It takes as input a certain number of CTFs and makes a balanced sampling of N images based on the defocus U values
+      - deep_center_predict: Center a set of particles in 2D using a neural network
+      - cl2d_clustering: 2D clustering protocol to group similar images (2D Averages or 2D Classes)
+
+   - Protocols updated
+      - flexalign: Added support for reading EER. Optimized and refactor the streaming, the continue action stabilized. FlexAlign can run multiple times in a single GPU or in multiple GPUs from within Scipion3.
+      - convert_pdb: now can read cif
+      - create_gallery: Allow Scipion protocol create gallery to access missing projection options
+      - ctf_consensus: optimized and refactor the streaming, the continue action stabilized. Remove parallelization
+      - movie_dose_analysis: optimized and refactor the streaming, the continue action stabilized
+      - movie_max_shift: optimized and refactor the streaming, the continue action stabilized, Remove parallelization
+      - tilt_analysis: optimized and refactor the streaming, the continue action stabilized
+      - subtract_projection: Adaptations for new logic in Xmipp program
+      - reconstruct_highres: Add GPU use for local angle assignment 
+
+   - Protocols fixed
+      -  trigger_data: Fix the way we split the output
+      -  subtract_projection: fnMask sub
+      -  classify_pca: Bug fix in the validate function
+      -  reconstruct_fourier: Fourier reconstruction now allows performing the CTF correction inside the same protocol.
+      -  volume_local_sharpening: local deblur performs now a single iteration by defaul
+      -  movie_max_shift: fixed with several parallel threads in streaming
+      -  reconstruct_highres: add unassigned vars fnVol1 fnVol2 to set loop
+      -  ctf_defocus_group: fix when testing multiple downsampling factors
+      -  ctf_micrographs: fix when testing multiple downsampling factors
+
+   - Protocols deprecated (For more details visit [this](https://github.com/I2PC/xmipp/wiki/Deprecating-programs-and-protocols))
+      - angular_resolution_alignment
+      - movie_opticalflow.py
+        
+   - More scipion-em-xmipp
+      - scikit-learn updated to 1.2
+      - protocols.conf list completed. All protocols are listed and clustered in Scipion
+
 ## Release 3.24.06 - Oceanus
    - New protocols
       - movie_alignment_consensus: protocol for the comparison of two global alignments
@@ -28,7 +70,7 @@
       - metaprotocol_golden_highres
       - solid_angle
       - split_volume
-   - More scipio-em-xmipp
+   - More scipion-em-xmipp
       - Solve Sonar Cloud reported bugs
       - Flexible import of pyQT on chimera script
       - Removing tkAgg matplotlib requirement in viewer_structure_map
@@ -58,7 +100,7 @@
       - classification_gpuCorr
       - classification_gpuCorr_full
       - classification_gpuCorr_semi
-   - More scipio-em-xmipp
+   - More scipion-em-xmipp
       - Updated Nvidia driver required version
 
 

{scipion-em-xmipp-24.6.0.0/scipion_em_xmipp.egg-info → scipion-em-xmipp-24.12.2}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 1.0
 Name: scipion-em-xmipp
-Version: 24.6.0.0
-Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
+Version: 24.12.2
+Summary: Plugin to use Xmipp programs within the Scipion framework (see https://xmipp.i2pc.es/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC
-Author-email: scipion@cnb.csic.es
+Author-email: xmipp@cnb.csic.es
 License: UNKNOWN
 Description: [![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-24.6.0.0 → scipion-em-xmipp-24.12.2}/requirements.txt

@@ -1,9 +1,11 @@
 scipion-pyworkflow>=3.0.31
-scikit-learn==0.22
+scikit-learn>=1.2
+scikit-image
 scipion-em
+scipion-app
 scipy<=1.10.0
 joblib
 peppercorn
 plotter
-scons
 PyWavelets
+

{scipion-em-xmipp-24.6.0.0 → scipion-em-xmipp-24.12.2/scipion_em_xmipp.egg-info}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 1.0
 Name: scipion-em-xmipp
-Version: 24.6.0.0
-Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
+Version: 24.12.2
+Summary: Plugin to use Xmipp programs within the Scipion framework (see https://xmipp.i2pc.es/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC
-Author-email: scipion@cnb.csic.es
+Author-email: xmipp@cnb.csic.es
 License: UNKNOWN
 Description: [![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-24.6.0.0 → scipion-em-xmipp-24.12.2}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -1,4 +1,4 @@
-CHANGES.md
+CHANGELOG.md
 LICENSE
 MANIFEST.in
 README.md
@@ -13,10 +13,12 @@ scipion_em_xmipp.egg-info/top_level.txt
 xmipp3/__init__.py
 xmipp3/base.py
 xmipp3/bibtex.py
+xmipp3/checkProtocolsConf.py
 xmipp3/constants.py
 xmipp3/programs.py
 xmipp3/protocols.conf
 xmipp3/utils.py
+xmipp3/version.py
 xmipp3/wizards.py
 xmipp3/xmipp_logo.png
 xmipp3/convert/__init__.py
@@ -28,8 +30,8 @@ xmipp3/protocols/protocol_align_volume.py
 xmipp3/protocols/protocol_align_volume_and_particles.py
 xmipp3/protocols/protocol_analyze_local_ctf.py
 xmipp3/protocols/protocol_angular_graph_consistency.py
-xmipp3/protocols/protocol_angular_resolution_alignment.py
 xmipp3/protocols/protocol_apply_alignment.py
+xmipp3/protocols/protocol_apply_tilt_to_ctf.py
 xmipp3/protocols/protocol_apply_transformation_matrix.py
 xmipp3/protocols/protocol_apply_zernike3d.py
 xmipp3/protocols/protocol_assignment_tilt_pair.py
@@ -37,6 +39,7 @@ xmipp3/protocols/protocol_break_symmetry.py
 xmipp3/protocols/protocol_center_particles.py
 xmipp3/protocols/protocol_cl2d.py
 xmipp3/protocols/protocol_cl2d_align.py
+xmipp3/protocols/protocol_cl2d_clustering.py
 xmipp3/protocols/protocol_classes_2d_mapping.py
 xmipp3/protocols/protocol_classify_pca.py
 xmipp3/protocols/protocol_classify_pca_streaming.py
@@ -52,6 +55,7 @@ xmipp3/protocols/protocol_ctf_correct_wiener2d.py
 xmipp3/protocols/protocol_ctf_defocus_group.py
 xmipp3/protocols/protocol_ctf_micrographs.py
 xmipp3/protocols/protocol_deep_center.py
+xmipp3/protocols/protocol_deep_center_predict.py
 xmipp3/protocols/protocol_deep_hand.py
 xmipp3/protocols/protocol_deep_micrograph_screen.py
 xmipp3/protocols/protocol_denoise_particles.py
@@ -66,12 +70,12 @@ xmipp3/protocols/protocol_generate_reprojections.py
 xmipp3/protocols/protocol_helical_parameters.py
 xmipp3/protocols/protocol_kerdensom.py
 xmipp3/protocols/protocol_local_ctf.py
+xmipp3/protocols/protocol_mics_defocus_balancer.py
 xmipp3/protocols/protocol_ml2d.py
 xmipp3/protocols/protocol_movie_alignment_consensus.py
 xmipp3/protocols/protocol_movie_dose_analysis.py
 xmipp3/protocols/protocol_movie_gain.py
 xmipp3/protocols/protocol_movie_max_shift.py
-xmipp3/protocols/protocol_movie_opticalflow.py
 xmipp3/protocols/protocol_movie_split_frames.py
 xmipp3/protocols/protocol_multiple_fscs.py
 xmipp3/protocols/protocol_multireference_alignability.py
@@ -155,15 +159,14 @@ xmipp3/tests/test_protocol_simulate_ctf.py
 xmipp3/tests/test_protocol_validate_fscq.py
 xmipp3/tests/test_protocol_validate_overfitting.py
 xmipp3/tests/test_protocols_add_noise.py
-xmipp3/tests/test_protocols_angular_resolution_alignment.py
 xmipp3/tests/test_protocols_continuousflex.py
 xmipp3/tests/test_protocols_deepVolPostprocessing.py
+xmipp3/tests/test_protocols_deepcenter_predict.py
 xmipp3/tests/test_protocols_deepres.py
 xmipp3/tests/test_protocols_fso.py
 xmipp3/tests/test_protocols_highres.py
 xmipp3/tests/test_protocols_local_defocus.py
 xmipp3/tests/test_protocols_localdeblur.py
-xmipp3/tests/test_protocols_mixed_movies.py
 xmipp3/tests/test_protocols_monores.py
 xmipp3/tests/test_protocols_realignment_classes.py
 xmipp3/tests/test_protocols_xmipp_2d.py
@@ -176,8 +179,9 @@ xmipp3/viewers/__init__.py
 xmipp3/viewers/plotter.py
 xmipp3/viewers/viewer.py
 xmipp3/viewers/viewer_analyze_local_ctf.py
-xmipp3/viewers/viewer_angular_resolution_alignment.py
+xmipp3/viewers/viewer_apply_tilt_to_ctf.py
 xmipp3/viewers/viewer_cl2d.py
+xmipp3/viewers/viewer_cl2d_clustering.py
 xmipp3/viewers/viewer_consensus_classes.py
 xmipp3/viewers/viewer_ctf_consensus.py
 xmipp3/viewers/viewer_deepEMHancer.py

{scipion-em-xmipp-24.6.0.0 → scipion-em-xmipp-24.12.2}/scipion_em_xmipp.egg-info/requires.txt

@@ -1,9 +1,10 @@
 scipion-pyworkflow>=3.0.31
-scikit-learn==0.22
+scikit-learn>=1.2
+scikit-image
 scipion-em
+scipion-app
 scipy<=1.10.0
 joblib
 peppercorn
 plotter
-scons
 PyWavelets

{scipion-em-xmipp-24.6.0.0 → scipion-em-xmipp-24.12.2}/setup.py

@@ -11,7 +11,8 @@ from setuptools import setup, find_packages
 from codecs import open
 from os import path
 
-from xmipp3 import XMIPP_URL, __version__
+from xmipp3 import XMIPP_URL
+from xmipp3.version import __version__
 
 here = path.abspath(path.dirname(__file__))
 
@@ -46,12 +47,12 @@ setup(
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version=__version__,  # Required
+    version=__version__[3:],  # Remove the "3" from the number version
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:
     # https://packaging.python.org/specifications/core-metadata/#summary
-    description='Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).',
+    description='Plugin to use Xmipp programs within the Scipion framework (see https://xmipp.i2pc.es/).',
 
     # This is an optional longer description of your project that represents
     # the body of text which users will see when they visit PyPI.
@@ -75,7 +76,7 @@ setup(
 
     # This should be a valid email address corresponding to the author listed
     # above.
-    author_email='scipion@cnb.csic.es',  # Optional
+    author_email='xmipp@cnb.csic.es',  # Optional
 
     # Classifiers help users find your project by categorizing it.
     #

{scipion-em-xmipp-24.6.0.0 → scipion-em-xmipp-24.12.2}/xmipp3/__init__.py

@@ -27,36 +27,59 @@
 # **************************************************************************
 
 import json
-import subprocess
 from datetime import datetime
-
-from pyworkflow import Config
 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 .base import *
-from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME
+from .version import *
+from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL
 
-type_of_version = 'release' #'devel'
-_logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
 
 _references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
-_currentBinVersion = '3.24.06.0'
-__version__ = _currentBinVersion[2:] + ".0"  # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
-
+_currentDepVersion = '1.0'
 # Requirement version variables
 NVIDIA_DRIVERS_MINIMUM_VERSION = 450
 
+type_of_version = version.type_of_version
+_logo = version._logo
+_binTagVersion = version._binTagVersion
+_pluginTagVersion= version._pluginTagVersion
+_currentDepVersion = version._currentDepVersion
+__version__ = version.__version__
+
+
 class Plugin(pwem.Plugin):
     _homeVar = XMIPP_HOME
     _pathVars = [XMIPP_HOME]
     _supportedVersions = []
     _url = XMIPP_URL
     _condaRootPath = None
-
+    # Refressing the plugin
+    # Inspects the call stack to find 'installPipModule' and sets 'self._plugin' to None.
+    # Uses CPython's internal API 'PyFrame_LocalsToFast' to sync changes.
+    # Risky and CPython-specific; use only if redesign is not possible.
+    try:
+        import inspect
+        import ctypes
+        for frameInfo in inspect.stack():
+            if frameInfo.function == "installPipModule":
+                frame = frameInfo[0]
+                frame.f_locals['self']._plugin = None
+                ctypes.pythonapi.PyFrame_LocalsToFast(
+				    ctypes.py_object(frame),
+				    ctypes.c_int(1))
+    except Exception as e:
+        print(e)
+    
     @classmethod
     def _defineVariables(cls):
-        cls._addVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
+        cls._defineEmVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
+        cls._defineVar(XMIPP_CUDA_BIN, pwem.Config.CUDA_BIN)
+        cls._defineVar(XMIPP_CUDA_LIB, pwem.Config.CUDA_LIB)
 
     @classmethod
     def getEnviron(cls, xmippFirst=True):
@@ -65,8 +88,8 @@ class Plugin(pwem.Plugin):
         pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
 
         environ.update({
-            'PATH': pwem.Config.CUDA_BIN,
-            'LD_LIBRARY_PATH': pwem.Config.CUDA_LIB
+            'PATH': cls.getVar(XMIPP_CUDA_BIN),
+            'LD_LIBRARY_PATH': cls.getVar(XMIPP_CUDA_LIB)
         }, position=pwutils.Environ.END)
 
         if os.path.isfile(getXmippPath('xmippEnv.json')):
@@ -117,94 +140,88 @@ class Plugin(pwem.Plugin):
             Scipion-defined software can be used as dependencies
             by using its name as string.
         """
+        
+        # Determine if we are on a development 
+        bundleDir = cls.__getBundleDirectory()
+        develMode = bundleDir is not None
+        
+        COMPILE_TARGETS = [
+            'dist/bin/xmipp_image_header', 
+            'dist/xmipp.bashrc'
+        ]
+        
+        # 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'
+        ]
+        
+        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))
+            env.addPackage(
+                'xmippDep', version=_currentDepVersion,
+                tar='void.tgz',
+                commands=commands.getCommands(),
+                neededProgs=['conda'],
+                default=False
+            )
+        
+        if develMode:
+            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
+        )
+        
+        ## EXTRA PACKAGES ##
+        installDeepLearningToolkit(cls, env)
 
-        ## XMIPP SOFTWARE ##
-        xmippDeps = []  # Deps should be at requirements.txt (old: scons, joblib, scikit_learn)
-
-        # Installation vars for commands formating
-        verToken = getXmippPath('v%s' % _currentBinVersion)
-        confToken = getXmippPath("xmipp.conf")
-        installVars = {'installedToken': "installation_finished",
-                       'bindingsToken': "bindings_linked",
-                       'verToken': verToken,
-                       'nProcessors': env.getProcessors(),
-                       'xmippHome': getXmippPath(),
-                       'bindingsSrc': getXmippPath('bindings', 'python'),
-                       'bindingsDst': Config.getBindingsFolder(),
-                       'xmippLib': getXmippPath('lib', 'libXmipp.so'),
-                       'coreLib': getXmippPath('lib', 'libXmippCore.so'),
-                       'libsDst': Config.getLibFolder(),
-                       'confToken': confToken,
-                       'strPlaceHolder': '%s',  # to be replaced in the future
-                       'currVersion': _currentBinVersion
-                       }
-
-        ## Installation commands (removing bindingsToken)
-        installCmd = ("cd {cwd} && {configCmd} && {compileCmd} N={nProcessors:d} && "
-                      "ln -srfn build {xmippHome} && cd - && "
-                      "touch {installedToken} && rm {bindingsToken} 2> /dev/null")
-        installTgt = [getXmippPath('bin', 'xmipp_reconstruct_significant'),
-                      getXmippPath("lib/libXmippJNI.so"),
-                      installVars['installedToken']]
-
-        ## Linking bindings (removing installationToken)
-        bindingsAndLibsCmd = ("find {bindingsSrc} -maxdepth 1 -mindepth 1 "
-                              r"! -name __pycache__ -exec ln -srfn {{}} {bindingsDst} \; && "
-                              "ln -srfn {coreLib} {libsDst} && "
-                              "touch {bindingsToken} && "
-                              "rm {installedToken} 2> /dev/null")
-        bindingsAndLibsTgt = [os.path.join(Config.getBindingsFolder(), 'xmipp_base.py'),
-                              os.path.join(Config.getBindingsFolder(), 'xmippLib.so'),
-                              os.path.join(Config.getLibFolder(), 'libXmipp.so'),
-                              installVars['bindingsToken']]
-
-        sourceTgt = [getXmippPath('xmipp.bashrc')]  # Target for xmippSrc and xmippDev
-        ## Allowing xmippDev if devel mode detected
+    @classmethod
+    def __getBundleDirectory(cls):
         # plugin  = scipion-em-xmipp  <--  xmipp3    <--     __init__.py
         pluginDir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
         # bundle  = xmipp-bundle  <-  src   <-  scipion-em-xmipp
         bundleDir = os.path.dirname(os.path.dirname(pluginDir))
 
-        isPypiDev = os.path.isfile(os.path.join(pluginDir, 'setup.py'))
-        isXmippBu = (os.path.isdir(os.path.join(bundleDir, 'src')) and
-                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
-        develMode = isPypiDev and isXmippBu
-        if develMode:
-            env.addPackage('xmippDev', tar='void.tgz',
-                           commands=[(installCmd.format(**installVars,
-                                                        cwd=bundleDir,
-                                                        configCmd='pwd',
-                                                        compileCmd='./xmipp all'),
-                                      installTgt+sourceTgt),
-                                     (bindingsAndLibsCmd.format(**installVars),
-                                      bindingsAndLibsTgt)],
-                           deps=xmippDeps, default=False)
-
-        avoidConfig = os.environ.get('XMIPP_NOCONFIG', 'False') == 'True'
-        alreadyCompiled = os.path.isfile(getXmippPath('v' + _currentBinVersion))  # compilation token (see the xmipp script)
-        configSrc = ('./xmipp check_config' if avoidConfig
-                     else './xmipp config noAsk && ./xmipp check_config')
-        env.addPackage('xmippSrc', version=_currentBinVersion,
-                       # adding 'v' before version to fix a package target (post-link)
-                       tar='xmippSrc-v' + _currentBinVersion + '.tgz',
-                       commands=[(installCmd.format(**installVars, cwd='.',
-                                                    configCmd=configSrc,
-                                                    compileCmd='./xmipp compileAndInstall'),
-                                  installTgt + sourceTgt),
-                                 (bindingsAndLibsCmd.format(**installVars),
-                                  bindingsAndLibsTgt)],
-                       deps=xmippDeps, default=not (develMode or alreadyCompiled))
-
-        ## EXTRA PACKAGES ##
-        installDeepLearningToolkit(cls, env)
-
-
+        isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
+                    os.path.isfile(os.path.join(bundleDir, 'xmipp')))
+        
+        return bundleDir if isBundle else None
+    
 def installDeepLearningToolkit(plugin, env):
 
     preMsgs = []
     cudaMsgs = []
     nvidiaDriverVer = None
-    useGpu = False
     if os.environ.get('CUDA', 'True') == 'True':
         try:
             nvidiaDriverVer = subprocess.Popen(["nvidia-smi",
@@ -221,7 +238,7 @@ def installDeepLearningToolkit(plugin, env):
                                 f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
                                 "set CUDA=True in 'scipion.conf' file")
                 nvidiaDriverVer = None
-        except (ValueError, TypeError):
+        except (ValueError, TypeError, FileNotFoundError):
             nvidiaDriverVer = None
             preMsgs.append("Not nvidia driver found. Type: "
                            " nvidia-smi --query-gpu=driver_version --format=csv,noheader")
@@ -230,6 +247,7 @@ def installDeepLearningToolkit(plugin, env):
             msg = ("Tensorflow installed without GPU. Just CPU computations "
                    "enabled (slow computations).")
             cudaMsgs.append(msg)
+            useGpu = False
 
     if nvidiaDriverVer is not None:
         preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)

scipion-em-xmipp-24.12.2/xmipp3/checkProtocolsConf.py

@@ -0,0 +1,117 @@
+# ***************************************************************************
+# * Authors:		 Carlos Oscar Sorzano (coss@cnb.csic.es)
+# *
+# *
+# * 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
+# * (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 'scipion@cnb.csic.es'
+# ***************************************************************************/
+'''
+Description: This script checks for any protocols missing in the file 
+             protocols.conf and lists them for further action.
+
+Usage: python check_missing_protocols.py
+'''
+
+import ast
+import glob
+import os
+
+def get_classes_from_file(file_path):
+    with open(file_path, 'r', encoding='utf-8') as file:
+        file_content = file.read()
+        tree = ast.parse(file_content)
+        class_names = [node.name for node in ast.walk(tree) if isinstance(node, ast.ClassDef)]
+        return class_names
+
+with open("protocols.conf", 'r', encoding='utf-8') as file:
+    protocolsConf = file.read()
+
+blackList = ['ScatterImageMarker','XMIPPCOLUMNS', 'XmippProtVolAdjBase', 'AlignVolPartOutputs','ProtPickingConsensusOutput',
+             'XmippProtEliminateEmptyBase', 'XmippProtDeepConsSubSet', 'XmippProtWriteTestP', 'NoOutputGenerated','XmippProtSubtractProjectionBase',
+             'XmippProtWriteTestC','KendersomBaseClassify','XmippProtAlignVolumeForWeb', 'XMIPPCOLUMNS', 'NoOutputGenerated', 'ScatterImageMarker',
+             'AlignVolPartOutputs']
+
+
+#######Missing classes
+missingCounter = 0
+classCounter = 0
+for py_file in glob.glob("protocols/*.py"):
+    for class_name in get_classes_from_file(py_file):
+        classCounter+=1
+        if not class_name in blackList:
+            if not class_name in protocolsConf:
+                print(f"Missing: {class_name} from {py_file}")
+                missingCounter +=1
+print(f"Missing classes: {missingCounter}/{classCounter}")
+
+
+
+#######Missing tests
+
+def extract_protocols_from_file(file_path):
+	"""Extrae las llamadas a self.newProtocol en un archivo."""
+	protocols = []
+	with open(file_path, 'r', encoding='utf-8') as f:
+		source_code = f.read()
+	tree = ast.parse(source_code)
+	for node in ast.walk(tree):
+		if isinstance(node, ast.Call):
+			if (isinstance(node.func, ast.Attribute) and
+					node.func.attr == "newProtocol" and
+					isinstance(node.func.value, ast.Name) and
+					node.func.value.id == "self"):
+				if node.args:
+					protocol_node = node.args[0]
+					if isinstance(protocol_node, ast.Name):
+						protocol = protocol_node.id
+					elif isinstance(protocol_node, ast.Attribute):
+						protocol = protocol_node.attr
+					elif isinstance(protocol_node, ast.Constant):
+						protocol = protocol_node.value
+					if protocol not in protocols:
+						protocols.append(protocol)
+	return protocols
+
+
+def extract_protocols_from_folder(folder_path):
+	"""Extrae todos los protocolos de los archivos .py en una carpeta."""
+	protocolsFull= []
+	for root, _, files in os.walk(folder_path):
+		for file in files:
+			if file.endswith(".py"):
+				file_path = os.path.join(root, file)
+				protocols = extract_protocols_from_file(file_path)
+				for protocol in protocols:
+					if protocol not in protocolsFull:
+						protocolsFull.append(protocol)
+	return protocolsFull
+
+folder_path = "tests/"
+protocols = extract_protocols_from_folder(folder_path)
+partProt = protocols.index('xpsp')
+protocols[partProt] = 'XmippProtScreenParticles'
+
+protocolsWithoutTest = []
+for py_file in glob.glob("protocols/*.py"):
+    for class_name in get_classes_from_file(py_file):
+	    if not class_name in blackList:
+		    if class_name not in protocols:
+			    protocolsWithoutTest.append(class_name)
+		    
+print(f"\nProtocolos without test ({len(protocolsWithoutTest)}/{len(protocols)})")
+print('\n'.join(protocolsWithoutTest))

{scipion-em-xmipp-24.6.0.0 → scipion-em-xmipp-24.12.2}/xmipp3/constants.py

@@ -28,10 +28,13 @@ This modules contains constants related to Xmipp3 protocols
 """
 
 # ------------------ Constants values --------------------------------------
+XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
 NMA_HOME = 'NMA_HOME'
 XMIPP_DLTK_NAME = 'deepLearningToolkit'  # consider to change it to xmipp_DLTK to make short it
+XMIPP_CUDA_BIN = 'XMIPP_CUDA_BIN'
+XMIPP_CUDA_LIB = 'XMIPP_CUDA_LIB'
 
 MASK_FILL_VALUE = 0
 MASK_FILL_MIN = 1