Pipeline: auto-documentation improvements#312

Merged

taimontgomery merged 18 commits intomasterfrom

issue-311

Jun 1, 2023

Commits on May 29, 2023

Adding "config" to the step listing in ResumeConfig classes so that the organize_config step and config_out_dir output are preserved.
AlexTate
committed
After further consideration, I'm updating tiny resume commands to write the updated Run Config back to the same location in the root directory of the Run Directory. This allows configurations to ca…
AlexTate
committed
Each configuration class has a new function: save_run_profile(). This function saves a copy of the file in the root of the Run Directory with amended paths. The idea is that these files should repr…
AlexTate
committed

Commits on May 30, 2023

Refactoring the functions that load config files to be more consistent. The function setup_file_groups() has been removed because it has been unnecessary since the introduction of the SampleSheet c…
AlexTate
committed
Updating ResumeConfig.load_paths_config() for backward compatibility with older Run Directories. These directories are upgraded to follow the new auto-documentation approach so that multiple resume…
AlexTate
committed
Updating Run Configs for new v1.5 spec. Also noticed that the Samples Sheet in START_HERE had sentence case in the Replicate Number column
AlexTate
committed
Bugfix for YamlShop.add_mapping(). Keys aren't listed in doc.ca.items under some circumstances.
AlexTate
committed
Updating ResumeCounterConfig._rebuild_entry_inputs(). These file lists need to be reset each time a resume run is performed. Also refactoring for cleaner code that's more consistent with the newer …
AlexTate
committed
Minor update to follow recommended usage of the csv module when passing in file objects.
AlexTate
committed
Minor consistency update for the FeatureSelector class and the timestamp_format regex
AlexTate
committed
Updating PathsSheet to remove the Samples Sheet from inputs that are forbidden to change from run to run. This allows users to change normalization settings if they wish. Nothing is stopping the us…
AlexTate
committed
Removing a redundant code block that snuck into a previous commit
AlexTate
committed
Updating documentation for the new auto-doc approach
AlexTate
committed
Merge branch 'master' into issue-311
AlexTate
committed

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Pipeline: auto-documentation improvements#312

Pipeline: auto-documentation improvements#312
taimontgomery merged 18 commits intomasterfrom
issue-311

Commits on May 26, 2023

Adding config directory creation as the first step of the workflow

Extending write_processed_config() to update the `processed_run_config` key in the config object before writing (but only if it is a run config based instance)

Updating ResumeConfig._add_timestamps() to create a timestamped config directory on resume runs

A processed and timestamped resume run config is now written to disk during resume runs when run_native=True. Previously this only happened when run_native=False.

Commits on May 29, 2023

Adding "config" to the step listing in ResumeConfig classes so that the organize_config step and config_out_dir output are preserved.

After further consideration, I'm updating tiny resume commands to write the updated Run Config back to the same location in the root directory of the Run Directory. This allows configurations to ca…

Each configuration class has a new function: save_run_profile(). This function saves a copy of the file in the root of the Run Directory with amended paths. The idea is that these files should repr…

Commits on May 30, 2023

Refactoring the functions that load config files to be more consistent. The function setup_file_groups() has been removed because it has been unnecessary since the introduction of the SampleSheet c…

Updating ResumeConfig.load_paths_config() for backward compatibility with older Run Directories. These directories are upgraded to follow the new auto-documentation approach so that multiple resume…

Updating Run Configs for new v1.5 spec. Also noticed that the Samples Sheet in START_HERE had sentence case in the Replicate Number column

Bugfix for YamlShop.add_mapping(). Keys aren't listed in doc.ca.items under some circumstances.

Updating ResumeCounterConfig._rebuild_entry_inputs(). These file lists need to be reset each time a resume run is performed. Also refactoring for cleaner code that's more consistent with the newer …

Minor update to follow recommended usage of the csv module when passing in file objects.

Minor consistency update for the FeatureSelector class and the timestamp_format regex

Updating PathsSheet to remove the Samples Sheet from inputs that are forbidden to change from run to run. This allows users to change normalization settings if they wish. Nothing is stopping the us…

Removing a redundant code block that snuck into a previous commit

Updating documentation for the new auto-doc approach

Merge branch 'master' into issue-311