Update RTD documentation. (docstrings, changelog, documentation refactors)

Description

1. Update Installation instructions. (Based on README.md)
2. Remove AGIPD64k from available detectors to calibrate.
3. Add changelog.rst
4. Expose cal_tools and xfel_calibrate functions' docstrings
5. Refactor the documentations.

How Has This Been Tested?

Relevant Documents (optional)

Types of changes

• Docs (changes to the documentation)
• Refactor (refactoring code with no functionality changes)

Checklist:

• I have updated the documentation accordingly.

Reviewers

@calibration

docs/source/changelog.rst

 Release Notes
 =============
 
-3.5.0a0
--------
-
-- [AGIPD] Support to correct only specific trains
-- [AGIPD] Use PPU device to select trains to correct
-- [AGIPD] Faster transposition of constants
-- [AGIPD] Add option to skip plots
-- Add option to skip report generation in xfel-calibrate
-- Add option to skip env freezing in xfel-calibrate
-- Add warning if xfel-calibrate output may not be reproducible
+3.5.5
+-----
+- [AGIPD][CORRECT] Set max tasks per worker to 1 to avoid Out Of Memory issue for AGIPD.
+
+3.5.4
+-----
+- [AGIPD] Convert bias_voltage parameter condition to integer in cal_tools.
+- [LPD] Fix correcting a single pulse.
+- [LPD] VCXI require 4 modules.
+
+3.5.3
+-----
+- [LPD][CORRECT] Optionally create virtual CXI files
+- [LPD][CORRECT] Expose max-nodes parameter
+- [AGIPD] Replace gain_choose_int by fused types
+- Fix missing install of restful_config.yaml
+- Fix use of xfel-calibrate --skip-report
+
+3.5.1
+-----
+- Calibration Constant version's new `Variant` file attribute. To indicate method of handling the constant post retrieval. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/619
+- Epix100 dark Badpixels Map. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/637
+- `skip-plots` flag to finish correction before plotting. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/635
+- First trainId's timestamp as RAW data creation_time, if there is myMDC connection. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/630
+- AGIPD correction can correct one cellId without plotting errors. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/642
+- Fixed mode relative gain constants in Jungfrau can be retrieved. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/639
+- Only instrument source is selected to check number of trains to dark process. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/636
+- AGIPD trains for dark processing is selected for each module individually. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/653
+- Produce report after trying to correct AGIPD run with no images. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/641
+- AGIPD's bias voltage for AGIPD1M is read from slow data. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/647
+- Removed psutil dependency. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/653
+- Update Pasha to 0.1.1 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/638
+
+3.5.0
+-----
+- Updating Correction and dark notebooks for JUNGFRAU: https://git.xfel.eu/detectors/pycalibration/-/merge_requests/518
+- Updating Correction and dark notebooks for AGIPD: https://git.xfel.eu/detectors/pycalibration/-/merge_requests/535
+- Updating Correction and dark notebooks for PnCCD: https://git.xfel.eu/detectors/pycalibration/-/merge_requests/559
+- Updating Correction and dark notebooks for ePix100: https://git.xfel.eu/detectors/pycalibration/-/merge_requests/500
+
+  * EXtra-data is integrated to read files in pycalibration for AGIPD, JUNGFRAU, ePix100, and PnCCD. Dark and Correction notebooks.
+  * Pasha is now used for processing data for JUNGFRAU, ePix100 and PnCCD.
+  * pyDetLib correction functions were removed (except for common-mode correction).
+  * `db-module` is useless now for JUNGFRAU, ePix100 and PnCCD. Some parameters were updated in dark and correction notebooks for the mentioned detectors.
+
+- `gain_mode` and burst mode are now available for JUNGFRAU. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/591
+- JUNGFRAU has now a new badpixel value, `WRONG_GAIN_VALUE`. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/591
+- Pass through available for testing in-progress ORCA service. https://git.xfel.eu/detectors/pycalibration/-/merge_requests?scope=all&state=merged&search=orca
+- Non-calibrated RAW h5files are no longer copied.
+- High priority partitions (`upex-high`and `upex-middle`) are used for runs from ACTIVE and READY proposals, only. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/628
+- Supporting to disable LPD Correction through the webservice. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/629
+- Compatibility for old DAQ files for REMI is added. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/607
+- server-overview refactors. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/593 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/589
+- AGIPD correction notebook support AgipdLitFrameFinder device. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/603
+- Parsing code arguments in xfel-calibrate is refactored. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/575
+- skip-plots option for AGIPD. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/581
+- Native implementation for transposition of constants AGIPD. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/580
+- Trains for AGIPD can be selected for correction. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/574
+- Skip report flag in xfel-calibrate. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/579
+- Fix ReadTheDocs. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/448
+- Fix error reporting for re-injecting the same CCV. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/627
+- Fix AGIPD for legacy runs without `gain_mode`. https://git.xfel.eu/detectors/pycalibration/-/merge_requests/617 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/626
+- Pinning markupsafe version 2.0.1 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/631
+- Pinning psutil 5.9.0 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/535
+- Updating Extra-data to 1.9.1 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/535
+- Updating h5py to 3.5.0 https://git.xfel.eu/detectors/pycalibration/-/merge_requests/602
 
 3.4.3
 -----