scipion-pyworkflow 3.6.0__tar.gz → 3.8.0__tar.gz

scipion_pyworkflow-3.8.0/CHANGES.txt

@@ -0,0 +1,400 @@
+V3.8.0
+users:
+  - Inform when a plugin does not import properly
+developers:
+  - Handling the name and the suffix to be used for a new output
+  - New method: Config.isCondaInstallation
+
+V3.7.0
+users:
+  - Add protocol is an icon.
+  - Right clik on canvas offers to add a protocol on the clicked location.
+  - Scipion log is a project.log (only for project events)
+  - Variables window saves non default variables changed (bug)
+  - Queue interoperability review:
+    - jobs cancelled in the queue are detected in scipion
+    - job and pids handling improved, pids = 0 when use queue for protocol rely on jobid
+    - Change Protocols Lock to Rlocks objects to avoid concurrency when updating the protocols jobid
+  - add information in the protocol log regarding execution type (pid or jobid)f
+  - Streaming protocols based on new streaming (generation steps) are resumable
+  - Avoiding a double process when launching a workflow using the protocol form
+  - pyworkflowtest tests fixed
+  - GUI will detect when protocols processes have been killed(cancelled) in all cases?
+  - fix outdated pyworkflow scripts
+  - scipion3 template (template manager) lists workflows at workflowhub.eu from "Scipion CNB" organization
+  - Join heterogeneous sets are possible for tomography objects TS and tomograms.
+developers:
+  - Canvas has a testing method: _drawGrid to draw a grid on the canvas (unused now)
+  - String.toSeconds:converts to seconds any "duration" string like "1h 4m 34s" -> 3600 + 240 + 34.
+  - ListDialog has a refresh method to refresh the content taking into account the filter
+  - Improve the DDBB lock in the method "_store". If Protocol._lock is locked, a nullcontext is used instead of another
+    Protocol._lock context, which causes a permanent lock.
+  - XmlMapper removed.
+  - FlatMapper instanatiation centralized:
+     New variable: SCIPION_MAPPER_USE_TEMPLATE. By default uses the template as it was now. If deacivated, instantiation happens on each iteration (less performant) but dev friendly
+  - Adding a parameter to launch jobs (e.g: bash)
+  - Handling item-click event in the treeview dialog
+  - Method copyAttributes expanded to manage the complex sets properly
+
+V3.6.0
+users:
+  - Window to see/edit config variables. Launched from Project menu in project window.
+  - Fix installation error: matplotlib imported at installation time
+  - Fixing an error drawing the graph
+developers:
+  - FileBrowser window tweaks: Can be called from a dialog.
+  - Windows can be called as dialogs with show(modal=True)
+  - askPath: Method to ask for a path (PATH, FOLDER or BASENAME)
+  - backup: Method in pyworkflow.utils.path to backup files
+  - All variables are centralized and Plugin._defineVar or _defineEmVar accept variable description, and type (VarTypes enum) to better describe the variable.
+  - ProgressBar handles the step in combination with increase method call
+  - Set.aggregate more flexible and versatile.
+        Accepts strings or lists in operations, labels or groupby args.
+        Accepts id or _objId ar fields
+  - String.getListFromValues: works now with strings with an x inside (e.g.: _x _y)
+  - New utils method: valueToList (converts the argument into a list if is not a list): Useful for "dual type arguments) that can be a list or not
+
+V3.5.0
+------
+users:
+  - New Icons.
+  - Icons based on sprites, easier to resize or customized
+  - New variable: SCIPION_SPRITES_FILE to point to a custom sprite. It should be compatible with sprites.png at pyworkflow/resources.
+  - Scipion GUI log moved to the log tabs and removed from menu
+  - New variable: SCIPION_SHOW_TEXT_IN_TOOLBAR, set it to anything to show the text of the icons below
+  - New variable: SCIPION_ICON_ZOOM, defaults to 50 (percent) to show icons at 16x16. 100 will set them to 32 or 75 to 24.
+  - Icons in toolbar grouped. Better row height adjustment in trees.
+  - Improved handling of the case where protocols steps are send to the queue, fix stop protocol functionality
+developers:
+  - ProjectConfig class removed
+  - New methods in path: hasChangedSince and isFileFinished
+  - New method in utils: strToDuration (useful to translate "1h 35m" to seconds). For duration parameters.
+  - New class Variable to be tested in Config class. A step towards a Config editing GUI.
+  - SCIPION_DEBUG_SQLITE rescued to activate SQL clauses in debug.
+  - Active jobs are stored in the 'jobIds' protocol variable. Iteration through these job IDs allows for canceling each active job sent to the queue.
+  - Implemented cleaning of old protocol job IDs and PIDs.
+  - Extending the ToolbarDialog buttons. Now is possible to define a tooltip and a shortcut
+  - Viewers has getName class method.
+  - Object.getClassName is now a class method
+  - Validating the Close method in the Dialog class. Now we can to reimplement de validateClose method.
+  - Better case-specific implementation of pID and jobID. Three scenarios: normal execution, sending the entire protocol to the queue, or sending individual steps.
+  - Object.clone a copy optionally clones the enable flag
+  - Set.getItem: returns the first item with a value in the fields passed. Useful for querying by TsId in tomo.
+  - Correctly update the protocols in streaming workflows when the input pointer points to a protocol, the protocol points to a set (i.e., classes), and this set points to another set (i.e., particles).
+
+V3.4.0
+------
+users:
+  - Prevent cyclic loops in protocols. Cannot chose as input, as output that is derived or will be derived from the current protocol.
+  - Tolerate cyclic loops saved projects projects, disconnecting the "problematic" protocol.
+developers:
+  - Dialog class: add lockGui input to allow the viewers to prevent getting the screen focus if desired.
+
+V3.3.1
+------
+users:
+  - Steps window can force finish steps too. Useful for some CS cases.
+  - "Continue workflow" from improved. Works with more cases.
+  - Fix output deletion when right-clicking on an output compatible with this option.
+developers:
+  - Set class has isItemEnabled to be used as callback based on item.isEnabled()
+  - config.py.OS class (not for GUI): to return distro info (isCentos or isUbuntu) or isWSL (--> new dependency "distro")"...
+
+V3.3.0
+------
+users:
+  - Boxes from Plugins in devel mode are prefixed with * now (not delta anymore)
+  - Partial exporting/copying will carry also the input of those protocols not being exported
+  - Partial importing/pasting will be linked to existing protocols in the project with the same id.
+  - Fix: Scheduling failed with direct pointers (impossible to get form GUI but programming or tests)
+  - tests: possible to use " tomo." (e.g.) to test just a plugin. Unfortunately needs adaptation in the launcher
+  - "Return" keypress "clicks" the active button in a window
+  - Avoid adding the same viewer twice
+
+developers:
+  - Control and Shift keypress are captured when clicking in analyze result button and passed to the viewer.
+  - Project.getProtocol() has a fromRuns mode to prevent going to the db. Used in a couple of calls.(performance)
+  - Plotter.createSubPlot: allow plots without axis passing xlabel and ylabel as None
+  - Tolerate type change in attributes in protocol execution processes.
+  - Fixing an error when loading a project where it is not possible to retrieve the current version of an installed plugin
+
+V3.2.0
+------
+users:
+  - Templates validate booleans properly (false, true, 0 or 1)
+  - Labels and box positions are saved after Labels being edited.
+  - scipion3 project list (or without list) should list existing projects.
+  - Windows are grouped by project under the project name.
+  - Do not allow empty Config variables unless is the default value
+  - SCIPION_MAIN_COLOR: If not valid, fallsback to Firebrick
+  - Project names: Only accepts digits, "letters", - or _. Rest are turned into -
+  - Fix wrong PARALLEL_COMMAND in hosts.conf created during tests.
+  - SCIPION_USE_QUEUE: New variable (default=False). If defined to anything else than False, new protocols will be sent to queue by default.
+
+developers:
+  - Tolerate loading of extra set properties but WARN the developer.
+  - ListDialog: allows for a preview panel on the right if previewCallback is passed.
+  - SQL DEBUG deprecated: active when regular debug is on.
+  - Boolean Config variables refactored to be "reversible".
+  - Show info id debug mode (print) when an infinite loop happens in the protocols graph
+V3.1.1
+------
+  - Hotfix: Fix resume single. Protocol was reset.
+
+V3.1.0
+------
+users:
+  - New optional config variable: SCIPION_MAIN_COLOR. Any medium tone color name or hexadecimal should work(like in CSS)
+  - New optional config variable: SCIPION_BG_COLOR. Any light tone color name or hexadecimal should work(like in CSS)
+  - Control + Plus (numpad) will increase the font of the logs. Control + subtract will restore it.
+  - Toolbar and actions refactored: Most of them have shortcuts and appear in the toolbar without text, but have tooltips showing the shortcut
+  - Plugins in devel mode are shown with a delta suffix after the package name.
+  - Green lines in log are lighter, colored lines are back in the log.
+  - Commands in the log are "announced" by "** Running command: **"
+  - Project list window: F5 on the filter box will refresh the list.
+  - Project list window: Auto refresh on window activate when data is older than 60 seconds
+  - New actions: Copy (Control+c) and Paste (Control +v) will allow to copy the selection to and from the clipboard.
+  - File browser thumbnail: Writes if the file is a link
+  - Protocol in devel mode is shown prefixing the protocol in the box and shown in log
+  - Unused graphical gui nodes are cleaned up upon protocols deletion and graph painting (to clean up old projects)
+  - Error in host.conf for clusters better described.
+  - Fixed a bug related to organizing the workflow when importing a template(Import workflow template option)
+  - Terminal where Scipion is being launched only shows ERROR level info. Rest goes to scipion.log shown by the Scipion log menu.
+  - Scipion windows of the same process are now grouped under the same icon. Window Tooltip says Scipion framework instead of Toplevel
+  - Refactoring Restart & Continue workflow option. Allowing to continue and restart a workflow from a protocol
+
+  
+ developers:
+  - Plugin.inDevelMode(): returns true is plugin installed in devel mode.
+  - Shortcut for devel mode is now Control+D since Control+d is for duplicate (old copy)
+  - Protocol.getClassPlugin deprecated. Use instead getPlugin()
+  - Protocol._cleanExtraFiles(): optional method to clean files other than tmp folder.
+  - Config.isScipionRunning(): To distinguish from just importing or running.
+  - Set implements copy() leaving mapper_path out.
+  - TaseCase: compareSetProperties() added to compare 2 set's properties.
+  - Add debugging messages to check the job status and add renameGpuIds method in the StepQueueExecutor
+
+V3.0.32
+-------
+  - Hotfix: fix links more versatile.
+V3.0.31
+-------
+  - Hotfix: Fixed updated protocol icon
+
+V3.0.30
+-------
+users:
+  - File browser: error while getting the preview thumbnail are reported as the preview string and logged.
+  - Wrong status when updating: When scheduling protocols, they were wrongly showed as failure temporarily.
+
+
+developers:
+  - Using logger in executor.py
+  - Fix: --overwrite problem. CONDA_ACTIVATION_CMD was disappearing form the config
+  - Fix: plugin manager error. wait.png renamed to wait.gif
+  - Improvement: Tolerate protocol loading when attribute type is changed by developers.
+  - CONDA_ACTIVATION_CMD is now a Config variable.
+  - Flag to indicate if steps list has new steps. Useful for new streaming approach.
+  - Base streaming protocol: ProtStreamingBase.
+
+V3.0.29
+-------
+users:
+  - Fix: with some host.conf, where current working dir is not "transferred" to the node, execution failed when
+    creating the logs cause they where relative. Now they (log paths) are passed to pw_protocol_run as absolute paths
+
+V3.0.28
+-------
+users:
+  - Fix: rare error making subsets of self referencing output.
+  - Schedule process: Logging starts from the very beginning. Better feedback when there is an error.
+  - Message is shown in project's info log when discovering viewers for the firs time.
+  - Fix: Expert level pointers not clearer anymore after copying or deacivating expert level.
+  - Protocol list output improved --> scipion3 protocols --with-doc
+  - Scheduling: more informative log lines.
+  - Exporting a workflow does not show the final confirmation dialog (just a log line)
+  - Font size responsive in file browser text box.
+developers:
+  - Fix: rare error when loading pointers with extended from the database
+  - More modules using logging: gui/project.py, mapper/sqlite.py
+  - Pointer.set: optional parameter to cancel extended reset. Used from mapper.
+  - Pyworkflow Domain now is operational. Still ED plugins needs adaptation.
+  - String class offers getListFromRange and getListFromValues for convenience when param any ot the Ranges
+  - getListFromValues, returns str list as before, but optionally you can pass a caster (int, float,..)
+  - GE validator: tolerates None values.
+  - Form.addBoolean() helper added to facilitate Boolean param definitions. TODO: Do it with the rest?
+  - dependencies updated
+  - icons changed to png 32, so transparency is understood by pillow latest version
+  - unused icons removed
+  - icon names all centralized in Icon class
+  - getImage: caches the images, rename gif to png.
+
+V3.0.27
+-------
+Users:
+ - Fixing an error refreshing the workflow:
+     * the protocol status changed intermittently
+ - "Use queue?" label and help reworded and linked to documentation site
+ - "Wait for" label and help reworded and linked to documentation site
+ - Fix: New protocols, without sibilings were wrongly located at the top.
+
+
+V3.0.26 (hotfix)
+-------
+ - Reporting url is now pointing to https.
+
+V3.0.25 (hotfix)
+-------
+ - Fix logger error when downloading a new dataset.
+
+V3.0.24 (hotfix)
+-------
+ - Do not fail when getting the size of an empty protocol.
+
+V3.0.23
+-------
+Users:
+ - Fixing a bug for static protocols: when a protocol had another protocol as input, it failed to wait until it had finished.
+ - Improvements in responsiveness to font size: Tables and automatic layouts. Object browser, Search windows.
+ - Filebrowser has 2 new shortcuts: "recent" and "Protocol folder"
+ - Text widget: "File does not exist message" removed.
+ - Rescue colors in terminal
+ - Rescue output in tests.
+ - New color mode: Size (GREEN < 1MB, ORANGE < 1GB, RED < 1TB, DARK > 1TB
+ - Color mode info is shown in the "info line" when switching
+ - Color mode age: fixed.
+ - New config variables:
+      SCIPION_LOG_FORMAT: Define log lines format base on python convention,
+      SCIPION_TEST_NOSYNC: Disable dataset syncing,
+      SCIPION_GUI_REFRESH_INITIAL_WAIT: Initial time to wait after a manual refresh. Defaults to 5.
+      SCIPION_GUI_CANCEL_AUTO_REFRESH: True will cancel automatic refreshes.
+ - scipion printenv returns also int variables.
+ - Tolerate project update errors (e.g.: read only filesystem due to quota + update)
+ - Check if scheduled process is alive when updating.
+
+Developers:
+ - Some modules switched to use logger instead of print: viewprotocols.py, browser.py and launch.py,
+   pw_schedule_run.py, viewprojects.py, canvas.py, project.py, protocol.py.
+ - LoggerConfigurator adapted to received logfile, flag for console handler and line format.
+ - pw_run_tests.py uses logging now.
+ - tests mode with --log now works. All goes to the same file and is not html.
+ - Protocol.getPath added = Protocol._getPath
+ - form.py, process.py, pw_sync_data.py, utils.py use logging now.
+ - All logging messages are affected by SCIPION_LOG_FORMAT (defaults to %(message)).
+ - stdout handler does exclude ERROR and CRITICAL messages.
+ - Test output can be sent to a log file (--log) and uses SCIPION_LOG_FORMAT.
+ - testdata --check-all renamed to --check and optionally can check a single dataset.
+
+V3.0.22
+-------
+ - Fixing a persistent error related with the logic of the EXECUTE/SCHEDULE button
+
+
+V3.0.21
+-------
+ - Generating an interface to create the scipion log file.
+ - Creating an option to display the scipion log
+ - New "Search protocol in graph" (Control + l) window to locate a box in the graph
+ - At loading time, selected protocol is "focused" (window scrolls to it)
+ - Control + MouseWheel scrolls horizontally
+ - Links are also detected when they are just "http"
+ - Bugfixed: Input list is shown when there are possible outputs and need to "expose details" (like selecting a specific volume in a set)
+ - Bugfixed: Outputs that a numeric do not break the "Browse object window"
+ - Fixing an error related with the logic of the EXECUTE/SCHEDULE button
+
+Developers:
+ - prerequisites could be just the id or the previous list of ids when adding a step.
+
+V3.0.20
+-------
+ - Empty sections/subsection (without protocols) in the left tree will not be shown
+
+Developers:
+ - Allow pointers to be defined with a list of classes instead of a string: "SetOfParticles, SetOfAverages" or [ SetOfParticles, SetOfAverages ]
+ - Two "utils" functions: hasAnyFileChanged, hasFileChangedSince to check if a file/s have changed since a "time" passed.
+ - BaseTest now has: setupTestOutput exposed --> self.setupTestOutput()
+ - Allow getting an item in a set not only by id but by a query: myset["_tsId=tomo1"].
+
+
+V3.0.19
+-------
+ - Scalar parameters pointing to outputs now works also when scheduling
+ - Fix: outputs after a Scalar output (boxSize from pickings) weren't offered to the chosen
+ - Defining a new format to handler the log
+ - Creating in the config new constants to prevent sqlite locks when updating any set
+    - SCIPION_UPDATE_SET_ATTEMPTS: Number of attempts when trying a set update. The default value is 3
+    - SCIPION_UPDATE_SET_ATTEMPT_WAIT: Time in seconds to wait between updates. The default value is 2 seconds
+
+Developers:
+ - In _showWizard, passing the paramName as a form variable so the wizard can check from which parameter it was called
+
+
+V3.0.18
+-------
+ - Fixed GUI errors:
+   - fixing the workflow collapse/expand nodes
+   - resetting nodes with manual subset looses the parent
+   - reporting the protocol wall time
+   - finished protocol can't be modified
+ - Fixed: execute a protocol directly that is not streaming and that has an open input must be scheduled
+ - Close all sets when stopping a protocol
+ - fixing an error closing some viewers(the action of closing some viewers closes Scipion completely)
+ - fixing an error drawing the protocols step tree
+ - fixing an error deleting a protocol by the keyboard
+ - logging DEBUG mode will be activated when toggling debug mode
+ - A dramatic plugin import error will be tolerated. Plugin will not be loaded.
+ - Possible outputs definition is now possible. Protocols can define possible outputs to allow designing
+   a workflow in advance without executing them.
+ - New variable added: SCIPION_STEPS_CHECK_SEC. Defaults to 3 (seconds). It represents how often new input is checked in streamified protocols. Increasing this   
+   value will relax the stress in the system, but will feel less "alive".
+ - Workflow templates can now be imported into an existing project
+
+Developers:
+ - Possible Outputs allowed: dict or enum definition possible, see Protocol._possibleOutput
+ - Allow readonly parameters in protocols. Useful in combination with wizards or just informative parameters.
+ - Added the variable SCIPION_PRIORITY_PACKAGE_LIST that is used in the view
+   protocols in order to load first the plugins that contains the main
+   protocols.conf sections. This variable is defined as string with the packages names separated by a space.
+   e.g: SCIPION_PRIORITY_PACKAGE_LIST = "pwem tomo cistem"
+
+
+v3.0.17
+-------
+ - Second tab of logs have just error messages (stderr output)
+ - Tests show stderr output too (last lines)
+ - Report host.conf submit command problems when parsing/formatting fails
+
+ Developers:
+ - Logging mechanism closer to a standard way. import logging + logging.getLogger() whould work in any module
+
+
+v3.0.16
+-------
+ - Do not suggest deleteing hosts-conf when parsing fails
+ - "Select from" option in context menu to select all protocols hanging from the current selection.
+ - Schedule optimized
+ - dataset download more verbose
+ - pyworkflow version shown in main project window
+ - new color chooser. More user friendly
+ - Viewers are not asked to open outputs generated by themselves. In case a viewer creates an output.
+ - File browser shows links
+ - File browser allow multiple file handlers for the same extension
+
+ Developers:
+ - weakImport tool: context manager to tolerate import errors
+
+-------
+v3.0.15
+-------
+ - Cancel fastcopy of shutil if SCIPION_CANCEL_FASTCOPY is defined (fix GPFS copying errors)
+ Developers:
+ - Allow renaming parameters using pyworkflow.protocol.params.DeprecatedParam
+
+-------
+v3.0.13
+-------
+
+April 21, 2021:
+ - GUI performance and speed up
+ - Improvement of the scheduling process
+ - Fixed the options: Restart, Continue, Reset and Stop a workflow

scipion_pyworkflow-3.8.0/MANIFEST.in

@@ -0,0 +1,6 @@
+ include *.rst
+ include *.txt
+
+# Include image files under resources
+ include pyworkflow/resources/*
+ include pyworkflow/resources/showj/*

{scipion_pyworkflow-3.6.0 → scipion_pyworkflow-3.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.6.0
+Version: 3.8.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna
@@ -8,33 +8,56 @@ Author-email: delarosatrevin@scilifelab.se, roberto@cnb.csic.es, gsharov@mrc-lmb
 Project-URL: Bug Reports, https://github.com/scipion-em/scipion-pyworkflow/issues
 Project-URL: Source, https://github.com/scipion-em/scipion-pyworkflow/
 Keywords: workflows science electron-microscopy cryo-em structural-biology image-processing scipion
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 License-File: LICENSE.txt
-Requires-Dist: bibtexparser<=1.2.0
-Requires-Dist: psutil<=5.9.1
-Requires-Dist: configparser<=5.2.0
-Requires-Dist: matplotlib==3.3.4; python_version == "3.6"
-Requires-Dist: matplotlib==3.5.2; python_version >= "3.7"
-Requires-Dist: numpy<=1.23.0
-Requires-Dist: pillow==8.4.0; python_version == "3.6"
-Requires-Dist: pillow==9.2.0; python_version >= "3.7"
-Requires-Dist: requests<=2.28.1
+Requires-Dist: bibtexparser<=1.4.1
+Requires-Dist: psutil<=5.9.6
+Requires-Dist: configparser==6.0.0; python_version >= "3.8"
+Requires-Dist: matplotlib==3.7.3; python_version == "3.8"
+Requires-Dist: matplotlib==3.8.1; python_version >= "3.9"
+Requires-Dist: pillow==10.1.0; python_version >= "3.8"
+Requires-Dist: numpy==1.24.4; python_version == "3.8"
+Requires-Dist: numpy==1.26.1; python_version >= "3.9"
+Requires-Dist: requests==2.31.0; python_version >= "3.8"
 Requires-Dist: tkcolorpicker
 Requires-Dist: distro<=1.8
+Requires-Dist: importlib-metadata<=6.8.0
 
-.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
-  :width: 200
-  :alt: Contributor Covenant
-  :target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/ 
+.. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: PyPI release
+
+.. image:: https://sonarcloud.io/api/project_badges/measure?project=scipion-em_scipion-pyworkflow&metric=alert_status
+        :alt: Quality Gate Status
+        :target: https://sonarcloud.io/summary/new_code?id=scipion-em_scipion-pyworkflow
+
+.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-pyworkflow?server=https%3A%2F%2Fsonarcloud.io
+        :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-pyworkflow
+        :alt: SonarCloud quality gate
+
+.. image:: https://img.shields.io/pypi/l/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: License
 
+.. image:: https://img.shields.io/pypi/pyversions/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: Supported Python versions
+
+.. image:: https://img.shields.io/pypi/dm/scipion-pyworkflow
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: Downloads
+
+.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
+        :alt: Contributor Covenant
+        :target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/
 
 pyworkflow
 ==========

{scipion_pyworkflow-3.6.0 → scipion_pyworkflow-3.8.0}/README.rst

@@ -1,8 +1,30 @@
-.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
-  :width: 200
-  :alt: Contributor Covenant
-  :target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/ 
+.. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: PyPI release
+
+.. image:: https://sonarcloud.io/api/project_badges/measure?project=scipion-em_scipion-pyworkflow&metric=alert_status
+        :alt: Quality Gate Status
+        :target: https://sonarcloud.io/summary/new_code?id=scipion-em_scipion-pyworkflow
+
+.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-pyworkflow?server=https%3A%2F%2Fsonarcloud.io
+        :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-pyworkflow
+        :alt: SonarCloud quality gate
+
+.. image:: https://img.shields.io/pypi/l/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: License
 
+.. image:: https://img.shields.io/pypi/pyversions/scipion-pyworkflow.svg
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: Supported Python versions
+
+.. image:: https://img.shields.io/pypi/dm/scipion-pyworkflow
+        :target: https://pypi.python.org/pypi/scipion-pyworkflow
+        :alt: Downloads
+
+.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
+        :alt: Contributor Covenant
+        :target: https://www.contributor-covenant.org/version/2/0/code_of_conduct/
 
 pyworkflow
 ==========

{scipion_pyworkflow-3.6.0 → scipion_pyworkflow-3.8.0}/pyworkflow/apps/pw_protocol_list.py

@@ -63,15 +63,11 @@ def hasDoubleInheritance(classRef):
 if __name__ == '__main__':
     count = 0
     withDoc = '--with-doc' in sys.argv
-    asciidoc = '--asciidoc' in sys.argv
     extended = '--extended' in sys.argv
+    ai = '--ai' in sys.argv
 
     emProtocolsDict = Config.getDomain().getProtocols()
-    emCategories = [('Imports', ProtImport, []),
-                    ('Micrographs', ProtMicrographs, []),
-                    ('Particles', ProtParticles, []),
-                    ('2D', Prot2D, []),
-                    ('3D', Prot3D, [])]
+
     protDict = {}
 
     # Group protocols by package name
@@ -90,10 +86,6 @@ if __name__ == '__main__':
             else:
                 protTuple = (k, v)
             protDict[packageName].append(protTuple)
-            for c in emCategories:
-                if issubclass(v, c[1]):
-                    c[2].append(protTuple)
-
 
     def iterGroups(protDict):
         groups = list(protDict.keys())
@@ -111,20 +103,7 @@ if __name__ == '__main__':
             print("* link:%s[%s]: %s" % (k, l, doc))
 
 
-    if asciidoc:
-        print(":toc:\n:toc-placement!:\n\ntoc::[]\n")
-
-        print("\n== By Categories\n")
-        for c in emCategories:
-            print("\n=== %s\n" % c[0])
-            printProtocols(c[2])
-
-        print("\n== By Packages\n")
-        for group, prots in iterGroups(protDict):
-            print("\n=== ", group, "(%d protocols)\n" % len(prots))
-            printProtocols(prots)
-
-    elif withDoc:
+    if withDoc:
         for group, prots in iterGroups(protDict):
             print("Package: ", group, "(%d protocols)" % len(prots))
             for p in prots:
@@ -144,6 +123,18 @@ if __name__ == '__main__':
                 for p in prots:
                     print(formatStr.format(group, p[0],
                                            p[1].getClassLabel(), *p[2:]))
+        elif ai:
+            for group, prots in iterGroups(protDict):
+                for protClassName, protClass in prots:
+                    print("\nThe protocol named \"%s\" can be found in the %s plugin." %(protClass._label, group))
+                    print("\"%s\" protocol help is as follows:\n %s." % (protClass._label, protClass.__doc__))
+                    instance = protClass()
+
+                    for name, param in instance._definition.iterParams():
+                        print("\"%s\" has a \"%s\" parameter that is explained as: %s" % (protClass._label, param.label, param.help))
+
+
+
         else:
             formatStr = "{:<15}\t{:<35}\t{:<35}"
             print(formatStr.format("PACKAGE", "PROTOCOL", "LABEL"))

{scipion_pyworkflow-3.6.0 → scipion_pyworkflow-3.8.0}/pyworkflow/config.py

@@ -87,12 +87,17 @@ class Variable:
         self.source = source
         self.value = value
         self.default = default
+        self.isDefault = isDefault if isDefault is not None else self._isValueDefault()
         self.var_type = var_type
-        self.isDefault = isDefault if isDefault is not None else value==default
     def setToDefault(self):
         self.isDefault=True
         self.value=self.default
 
+    def setValue(self, new_value):
+        self.value = new_value
+        self.isDefault= self._isValueDefault()
+    def _isValueDefault(self):
+        return self.value==self.default
 class VariablesRegistry:
     _variables={}
 
@@ -272,6 +277,10 @@ class Config:
 
     SCIPION_NOTES_ARGS = _get(SCIPION_NOTES_ARGS, None)
 
+    # External text editor:
+    SCIPION_TEXT_EDITOR = _get(SCIPION_TEXT_EDITOR, '',
+    "Preferred text editor executable.", caster=str)
+
     # Aspect
     SCIPION_FONT_NAME = _get('SCIPION_FONT_NAME', "Helvetica",
     "Name of the font to use in Scipion GUI. Defaults to Helvetica.")
@@ -346,6 +355,10 @@ class Config:
        2: Run a single protocol
        3: Run a sub-workflow """, caster=int)
 
+    SCIPION_MAPPER_USE_TEMPLATE = _get('SCIPION_MAPPER_USE_TEMPLATE', TRUE_STR,
+    "Set it to False to force instantiation for each item during sets iterations. Experimental. This penalize the iteration but avoids"
+    "the use of .clone() ot the items.") == TRUE_STR
+
     try:
         VIEWERS = ast.literal_eval(_get('VIEWERS', "{}", "Json string to define which viewer are the default ones per output type."))
     except Exception as e:
@@ -514,6 +527,25 @@ class Config:
         like registering FileHandlers or other stuff not needed when just importing modules."""
         return cls.SCIPION_HOME_DEFINED != False
 
+    @classmethod
+    def isCondaInstallation(cls):
+        """ Returns true if the scipion installation is done using conda"""
+
+        # Get the CONDA_PYTHON_EXE
+        # NOTE: This will not work when calling scipion python directly! But should works using the launcher.
+        envFolder = os.environ.get("CONDA_PREFIX", None)
+
+        # No conda variable... virtualenv installation!!
+        if envFolder is None:
+            return False
+        else:
+            from pyworkflow.utils import getPython
+            # Conda available.... let's check if it is active the same scipion env
+            condaExe = os.path.join(envFolder, "bin", "python")
+            return condaExe == getPython()
+
+
+
 
 # Add bindings folder to sys.path
 sys.path.append(Config.getBindingsFolder())