scipion-em-xmipp 26.1.0__tar.gz → 26.2.0__tar.gz

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/CHANGELOG.md

@@ -1,3 +1,11 @@
+## Release 26.2.0
+- More scipion-em-xmipp
+   - xmipp3-installer package installed from pypi, reverting previous temporal fix
+   - Added new dependencie to solve error with libicu18
+ 
+- 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)))
+   - DeepCenter
+  
 ## Release 26.1.0
 - Protocols updated
   - deep_micrograph_cleaner: Showing thumbnails of micrographs with the mask and the coordinates stamps

{scipion_em_xmipp-26.1.0/scipion_em_xmipp.egg-info → scipion_em_xmipp-26.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 26.1.0
+Version: 26.2.0
 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)
@@ -17,6 +17,7 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
+Requires-Dist: xmipp3-installer<3.0.0,>=2.0.4
 Requires-Dist: numpy==1.*
 Dynamic: license-file
 

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/requirements.txt

@@ -5,5 +5,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
-#xmipp3-installer>=2.0.4,<3.0.0
+xmipp3-installer>=2.0.4,<3.0.0
 numpy==1.*

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0/scipion_em_xmipp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 26.1.0
+Version: 26.2.0
 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)
@@ -17,6 +17,7 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
+Requires-Dist: xmipp3-installer<3.0.0,>=2.0.4
 Requires-Dist: numpy==1.*
 Dynamic: license-file
 

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/scipion_em_xmipp.egg-info/SOURCES.txt

@@ -37,6 +37,8 @@ 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_center.py
+xmipp3/legacy/protocols/protocol_deep_center_predict.py
 xmipp3/legacy/protocols/protocol_deep_denoising.py
 xmipp3/legacy/protocols/protocol_enrich.py
 xmipp3/legacy/protocols/protocol_extract_particles_movies.py
@@ -104,8 +106,6 @@ xmipp3/protocols/protocol_ctf_correct_phase.py
 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

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/scipion_em_xmipp.egg-info/requires.txt

@@ -5,4 +5,5 @@ joblib
 peppercorn
 plotter
 PyWavelets
+xmipp3-installer<3.0.0,>=2.0.4
 numpy==1.*

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/xmipp3/__init__.py

@@ -160,7 +160,8 @@ class Plugin(pwem.Plugin):
             "libjpeg-turbo",
         ]
 
-        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng"
+        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng "
+        CONDA_ICU_PACKAGE = 'icu=72'
 
         if Config.isCondaInstallation():
             condaEnvPath = os.environ['CONDA_PREFIX']
@@ -168,7 +169,7 @@ class Plugin(pwem.Plugin):
 
             commands = CondaCommandDef(scipionEnv, cls.getCondaActivationCmd())
             #commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
-            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE)
+            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE + CONDA_ICU_PACKAGE)
             commands.touch("deps_installed.txt")
             env.addPackage(
                 'xmippDep', version=_currentDepVersion,
@@ -177,15 +178,12 @@ class Plugin(pwem.Plugin):
                 neededProgs=['conda'],
                 default=True
             )
-        xmipp3_installer_cmd = f'pip install "xmipp3-installer @ git+{XMIPP3_INSTALLER_URL}@{_xmipp3_installerV}" '
         if develMode:
             xmippSrc = 'xmippDev'
             installCommands = [
-		        (f'{xmipp3_installer_cmd } && '
-				 f'cd {pwem.Config.EM_ROOT} && rm -rf {xmippSrc} && '
+		        (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)
 	        ]
 
@@ -200,8 +198,7 @@ class Plugin(pwem.Plugin):
         else:
             xmippSrc = f'xmipp3-{version._binVersion}'
             installCommands = [
-                (f'{xmipp3_installer_cmd } && '
-				 f'cd .. && rm -rf {xmippSrc} && '
+                (f'cd .. && rm -rf {xmippSrc} && '
                  f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
                  f'cd {xmippSrc} && '
                  f'./xmipp', COMPILE_TARGETS)

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/xmipp3/protocols/__init__.py

@@ -133,6 +133,4 @@ from .protocol_volume_consensus import XmippProtVolConsensus
 from .protocol_volume_local_adjust import XmippProtLocalVolAdj
 from .protocol_classes_2d_mapping import XmippProtCL2DMap
 from .protocol_deep_hand import XmippProtDeepHand
-from .protocol_deep_center import XmippProtDeepCenter
 from .protocol_compute_likelihood import XmippProtComputeLikelihood
-from .protocol_deep_center_predict import XmippProtDeepCenterPredict

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/xmipp3/protocols.conf

@@ -63,8 +63,6 @@ Protocols SPA = [
 	{"tag": "section", "text": "2D", "children": [
 		{"tag": "protocol_group", "text": "Align", "openItem": "False", "children": [
 			{"tag": "protocol", "value": "XmippProtCL2DAlign",   "text": "default"},			
-			{"tag": "protocol", "value": "XmippProtDeepCenter",   "text": "default"},
-			{"tag": "protocol", "value": "XmippProtDeepCenterPredict",   "text": "default"},
 			{"tag": "protocol", "value": "XmippProtApplyAlignment",   "text": "default"},
 			{"tag": "section", "text": "more", "openItem": "False", "children": [
 				{"tag": "protocol", "value": "ProtAlignmentAssign", "text": "default"}

{scipion_em_xmipp-26.1.0 → scipion_em_xmipp-26.2.0}/xmipp3/version.py

@@ -40,6 +40,6 @@ _binVersion = 'v4' # Increase it if major release is generated in xmipp
 # - If several of the above are true, only change the biggest one applicable (
 #   for example, if a fix is made and a new protocol are included in the same
 #   pull request, increase the one related to the new protocol).
-__version__ = '26.1.0'
+__version__ = '26.2.0'
 
-_currentDepVersion = '1.0'
+_currentDepVersion = '1.1'