3.11.2:
 Users:
  - Correct fix in odd / even when only tomographic reconstruction is requested (Thanks Rory!).
  - Set the default no. threads to 3.
 Developers: remove the dependency on ProtTomoBase.
3.11.1: deploy test.
3.11.0:
 Users: interpolated tilt-series removed. The viewers manage from scipion-em-tomo 3.10.1 the interpolation.
 Developers:
  - Adapted to the updated TiltSeries model from scipion-em-tomo 3.10.1.
  - Streaming reviewed and made more robust.
  - Interpolated tilt-series checking removed from the tests.
  - Fix streaming condition to insert the closing step. Now it uses collections.Counter when comparing
    the tsId lists instead of direct comparison, which is order-sensitive.
3.10.3:
 Users:
  - Fix the even/odd functionality.
3.10.2:
 Users:
  - Fix odd/even functionality.
  - Fix the write aln file method so it works no matter if the tilt-series header identifies it as a stack
    or as a volume.
 Developers:
  - Add some preventing locks in the steps generator step to prevent the recursive use of cursors that makes
    streamified protocols to close the output before expected.
  - Replace the setup.py by the corresponding pyproject.toml.
  - Improve the method readingOutput.
  - Improve robustness in streaming: check the tilt-series size before inserting the steps.
3.10.1:
 Users:
  - Fix: re-align aligned tilt-series after having excluded views is now possible (validation is now a warning).
3.10.0:
 Users:
  - Add input tilt-series excluded views management.
  - Add odd/even tomograms reconstruction,
  - Fix: amplitude contrast is read from the tilt-series metadata and passed to AreTomo.
  - Do not support old AreTomo versions.
 Developers:
  - Write new tests with a better characterized test dataset.
  - Tests renewed with a better adapted (real dark frames) test dataset and with cases of TS with excluded views.
  - Add needsgpu attribute to the steps generation.
  - Aln file writer method added to adapt the plugin to the API of AreTomo2-1.1.3 when only reconstructing the tomograms.
  - Fix indirect pointers.
3.9.5: add aretomo2 1.1.3
3.9.4: set aretomo2 1.0.0 as default, because 1.1.2 has broken remove dark option
3.9.3: hotfix: _defineVariables method must be a class method to be compatible with scipion command config -p
3.9.2:
   - Aretomo does nos fail when closing its output when process is killed
   - Listed protocol's names are defaults ones.
   - Tolerate failed tilt-series, avoiding the protocol interruption and generating a specific output for the failed
     tilt-series.
   - Force enable DW when saving extra IMOD output
  Developers:
   - Steps now use the tsId instead of the objId.
3.9.1:
  Users:
   - Add aretomo2 1.1.2
   - Fix backwards compatibility.
   - Add an option to specify AlignZ per TS.
   - fix dose weighting bug related to the tilt angle file (aretomo2 only)
  Developers:
   - The tests now use the Test Centralization Layer update and expansion of the used test set definition
     from em-tomo v3.6.0.
   - Update the acquisition order in the CTFTomo objects (field added to that class in scipion-em-tomo v3.7.0).
3.9.0:
  Users:
    - The protocol form now present CTF-related parameters, to choose if estimate it or
      not and phase plate acquisition related params (estimate the phase shift).
    - Generates the output SetOfCtfTomoSeries if the CTF files are found
    - Add dataimport module to parse the CTF generated so it can be called from the
      centralized protocol for importing CTFs.
    - Fix the origin set by Scipion to the generated tomograms.
    - Outputs are not stored in case the are not correctly generated.
    - If dose-weighting active, the accumulated dose of the interpolated TS is set to zero  to avoid double dose
      correction if using the interp TS for the PPPT.
  Developers:
    - Rewrite tests using the TCL from em-tomo and the reliontomo test dataset.
3.8.3: typo bugfix
3.8.2: bugfix: tomograms origin fixed and more robust
3.8.1: bugfix for reading aln file with dark views removed
3.8:
    - add aretomo2 1.0.0
    - fix output aln file parsing during local alignment
    - add extra output option
3.7.2:
 - minor changes
 - Fix origin of tomograms when there is binning.
3.7.1: fix pw requirements
3.7  : initial streaming support (@albertmena)
3.6.5: allow unsorted tilt series
3.6.4: adding type hints
3.6.3: reduce number of Set[item] calls
3.6.2:
 - fix applyTransform in the convert step
 - add interpolated flag
3.6.1:
 - add aretomo 1.3.4, remove support for versions < 1.1.0
 - fix alignment matrix for excluded TS views
3.6:
 - set tilt axis angle to 0 for interpolated aligned TS (fixed issue #36)
 - remove updateDim calls
 - use Acquisition from TS for new tomo objs
3.5.1: add aretomo 1.3.3
3.5:
 - get rid of xf file conversion, use aln directly
 - add aretomo 1.3.0
 - update citation
3.4: always output stack with alignment info
3.3: scaling should not be applied to transforms, as xf refers to original TS
3.2:
 - fixed output TS shifts scaling when using binning
 - hide flip volume option when not making a tomo
 - guess cuda version
3.1:
 - add possible outputs class
 - two default TS outputs: aligned (interpolated) TS and original (with alignment metadata)
 - added DarkTol parameter to GUI
 - add AreTomo 1.2.5
3.0.16 - add AreTomo 1.2.5
3.0.15 - add possible outputs class
3.0.14 - AreTomo 1.2.0 added
3.0.13 - fix default installed version
3.0.12 - AreTomo 1.1.1 added, now can use previous alignment as input
3.0.11 - AreTomo 1.1.0 added
3.0.10 - parse and save tilt angles correctly
3.0.9 - remove tilt axis angle from GUI, fix validation, fix accum.dose and dose weighting
3.0.8 - fix output TS file loc index
3.0.7 - fix bug: writing output alignment info to an already aligned TS
3.0.6 - fix dose-weighting error, update citation
3.0.5 - added refine tilt angles param for 1.0.12+
3.0.4 - added refine tilt axis param, switch off volume flip for v1.0.12+
3.0.3 - bug fixes (reported by Bram Koster)
3.0.2 - add version 1.0.12
3.0.1 - add version 1.0.10
3.0.0 - first version of the plugin
