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@martinkilbinger martinkilbinger commented Mar 25, 2022

Summary

Removed obsolete config files (still to be found on https://github.com/CosmoStat/shapepipe/tree/unreleased_content branch).

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  • Documentation has been added/updated consistently with the code
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@sfarrens sfarrens merged commit b2a69ae into develop Mar 29, 2022
@sfarrens sfarrens deleted the conf_clean_up branch March 29, 2022 08:06
sfarrens added a commit that referenced this pull request Apr 1, 2022
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
sfarrens added a commit that referenced this pull request Apr 1, 2022
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

* final clean up

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
sfarrens added a commit that referenced this pull request Sep 17, 2022
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <[email protected]>

Co-authored-by: Martin Kilbinger <[email protected]>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <[email protected]>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* PR suggestions

Co-authored-by: Samuel Farrens <[email protected]>

* update patch version

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>
sfarrens added a commit that referenced this pull request Oct 12, 2022
* Summer 2022 Patch Release v1.0.1 (#581)

* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <[email protected]>

Co-authored-by: Martin Kilbinger <[email protected]>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <[email protected]>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* PR suggestions

Co-authored-by: Samuel Farrens <[email protected]>

* update patch version

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>

* fixed typo in variable name

* config file vignet runner output fixed

* typo in make_cat config ini file fixed

Co-authored-by: Samuel Farrens <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>
sfarrens added a commit that referenced this pull request Oct 12, 2022
* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <[email protected]>

Co-authored-by: Martin Kilbinger <[email protected]>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <[email protected]>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* PR suggestions

Co-authored-by: Samuel Farrens <[email protected]>

* update patch version

* random runner: hp masks working; doc updated (#580)

* random runner: hp masks working; doc updated

* random runner config file updated

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* passing tests

* Update shapepipe/modules/random_cat_package/__init__.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/__init__.py

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* Bug fix(es) for v1.0.1 (#586)

* Summer 2022 Patch Release v1.0.1 (#581)

* added CD GitHub action

* fixed bug in RunLog class (#548)

* 800deg2 (#544)

* added config files for matching 800deg2 survey

* Added Xavier as contributor; match external catalogue fix

* match 800

* match_ext: output distance

* match_ext output_dist def value

* Tutorial documentation (#543)

* updating job script and tutorial

* tutorial; fix config file

* tutorial finished

* no change

* psfex update (minor bug)

* psfex running

* updated MCCD config files

* comment in config file

* config file fix for MCCD

* config file fix for MCCD

* removed unused option in usage str

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* improved tutorial according to PR review

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* tutorial clean-up

* post_proc cleaned up; tutorial added output dir names

* changes to tutorial, post-proc and mccd plot doc

* get_images error msg testing

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* Update docs/source/pipeline_tutorial.md

Co-authored-by: Samuel Farrens <[email protected]>

* removed prompt from bash example

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

* PR review changes to doc

* PR review changes to doc

* Update docs/source/post_processing.md

Co-authored-by: Samuel Farrens <[email protected]>

Co-authored-by: Samuel Farrens <[email protected]>

* added contribution guidelines (#550)

* added contribution guidelines

* Update CODE_OF_CONDUCT.md

* tutorial bugfixes (#552)

Co-authored-by: Lucie Baumont <[email protected]>

* removed pep8 error exceptions (#554)

* Understanding the API docs (#553)

* added md for understanding the api docs

* updates following reviwer comments

* Update package versions (#539)

* updated doc-tests

* updated package versions

* pin documentation packages

* updated ShapePipe version and cleaned up

* Config file clean up (#556)

* Removed unused config files in example/cfis

* Removed obsolete config dirs tutorial and ps3pi_cfis

* removed old unions config files

* Update docs/source/configuration.md

Co-authored-by: Martin Kilbinger <[email protected]>

* final clean up

* removed obsolete distance-based overlap region flagging

* removed errornous mccd_interp_runner call

* Added Tobias' MCCD plot config file to validate joint cat

* Added Tobias' MCCD plot config file to validate joint cat

* removed duplicate config file

* Random catalogue improvements (#570)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* Updated docs and references (#579)

* updated docs and references

* Update docs/source/module_develop.md

Co-authored-by: Martin Kilbinger <[email protected]>

Co-authored-by: Martin Kilbinger <[email protected]>

* Random runner updates (#573)

* merge_final script: added option for additional tile ID path to select tiles; clean-up

* typo in doc string

* started to implement healpix mask output

* healpix options for random/mask

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/random_cat_package/random_cat.py

Co-authored-by: Samuel Farrens <[email protected]>

* Modifications for PR review

* comments from PR review

Co-authored-by: Samuel Farrens <[email protected]>

* added masking for NGC objects (#575)

* added masking for NGC objects

* debugging ngc np binary file

* Fixed bugs in new mask handling (input FITS files)

* debug info to log file for checking existing images

* mask: combined dso masks into dictionary

* PR edits

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* added symlink

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/modules/mask_package/mask.py

Co-authored-by: Samuel Farrens <[email protected]>

* Update shapepipe/pipeline/file_io.py

Co-authored-by: Samuel Farrens <[email protected]>

* PR suggestions

Co-authored-by: Samuel Farrens <[email protected]>

* update patch version

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>

* fixed typo in variable name

* config file vignet runner output fixed

* typo in make_cat config ini file fixed

Co-authored-by: Samuel Farrens <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>

* fixed blank lines

Co-authored-by: Martin Kilbinger <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Lucie Baumont <[email protected]>
Co-authored-by: Tobias Liaudat <[email protected]>
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