ccdutils issueshttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues2018-05-10T12:46:39Zhttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/42Method duplicitation in the file test_process_components_cif_cli.py2018-05-10T12:46:39ZIjaz AhmadMethod duplicitation in the file test_process_components_cif_cli.pyThe method `test_subdir_in_files_created(output_dir, subdir)` is defined twice in the fileThe method `test_subdir_in_files_created(output_dir, subdir)` is defined twice in the filerefactor ccd_utils with better class structure.Oliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/41Get process_components_cif_cli working in refactoring branch2018-10-13T09:17:51ZOliver SmartGet process_components_cif_cli working in refactoring branchIssue #38 *Add process_components_cif script to back refactoring branch in stub form* now finished.
So functionality developed and tested in milestone %1 can now be added back to refactoring branch using the unit test [test_process_comp...Issue #38 *Add process_components_cif script to back refactoring branch in stub form* now finished.
So functionality developed and tested in milestone %1 can now be added back to refactoring branch using the unit test [test_process_components_cif_cli.py](pdbeccdutils/tests/test_process_components_cif_cli.py) taken from current master.refactor ccd_utils with better class structure.https://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/40Docstring format and automatic python API documenation generation2018-04-18T10:10:49ZOliver SmartDocstring format and automatic python API documenation generationIt would be useful to agree on docstring format.It would be useful to agree on docstring format.refactor ccd_utils with better class structure.Lukas PravdaLukas Pravdahttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/39Agree coding standards2018-06-01T08:36:42ZOliver SmartAgree coding standardsFor the refactoring work it would be a good idea to agree on coding standards.
* Code to PEP8 compliant.
* Unit tests to use pytest rather than nose as this is much easier to use in practice (and not out of date)
although pytest suppor...For the refactoring work it would be a good idea to agree on coding standards.
* Code to PEP8 compliant.
* Unit tests to use pytest rather than nose as this is much easier to use in practice (and not out of date)
although pytest supports yield in tests (currently used a lot) this is deprecated and some this will be replaced by parameterised tests. refactor ccd_utils with better class structure.https://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/38Add process_components_cif script to back refactoring branch in stub form2018-03-31T14:35:20ZOliver SmartAdd process_components_cif script to back refactoring branch in stub formThe script `process_components_cif` was the major product of the initial ccd_utils project milestone \#1 %1 that was completed in September 2017.
Project milestone \#3 %3 is to completely replace the code in the initial project but p...The script `process_components_cif` was the major product of the initial ccd_utils project milestone \#1 %1 that was completed in September 2017.
Project milestone \#3 %3 is to completely replace the code in the initial project but process_components_cif` is a well considered script that achieved its aims:
```
Script for PDBeChem backend infrastructure.
Processes the wwPDB Chemical Components Dictionary file components.cif
producing files for
http://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/
To do this components.cif is split into individual PDB chemical component
definitions cif files, sdf files, pdb files and image files.
In addition creates chem_comp.xml and chem_comp.list for all components.
```
The unit tests [test_process_components_cif_cli.py](pdbeccdutils/tests/test_process_components_cif_cli.py) are worth updating and preservingrefactor ccd_utils with better class structure.Oliver SmartOliver Smarthttps://gitlab.ebi.ac.uk/pdbe/ccdutils/-/issues/37Create unit tests for new refactoring branch2018-05-22T13:22:42ZOliver SmartCreate unit tests for new refactoring branch* Unit tests required
* Very often these can be can based on original ccd_utils tests in many places.
* but nose is rather cumbersome
* use pytest in stead
* do not nose yield mechanism to create sub tests.
* separate tests using classe...* Unit tests required
* Very often these can be can based on original ccd_utils tests in many places.
* but nose is rather cumbersome
* use pytest in stead
* do not nose yield mechanism to create sub tests.
* separate tests using classes to group related tests as this makes things much clear.
* Writing tests will mean that @oliversmart will become familiar with coderefactor ccd_utils with better class structure.Oliver SmartOliver Smart