Scipion-pyworkflow

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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.

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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.

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- Reporting url is now pointing to https.

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- Fix logger error when downloading a new dataset.

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- Do not fail when getting the size of an empty protocol.

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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.