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Remove debug print hello in to_idt_bulk_input_format
* Fixes #163; Remove Helix.pitch and Helix.yaw Completed: * Remove Helix.pitch and Helix.yaw * Update Design.from_json to be compatible with designs that specified pitch and yaw in individual Helix (except when multiple helices in the same group have different pitch/yaw values, in which case, IllegalDesignError is raised) * Updated examples that used pitch and roll * Updated unit tests that used pitch/roll * Added new unit test to test new Design.from_json * Add Design method for looking up pitch/yaw/roll for helices
Using re.sub (re is already imported), along with a replacement function that pulls from the replacement map, avoids repeated string replacements within Python and significantly speeds up encoding for large files. Note that I think this will raise a KeyError if the user has something with a name fitting "@@(\d+)@@" where the number is larger than the largest unique_id, and will corrupt the file if it is not. However, this is similar to the current situation.
Encoder indent suppression: str.replace → re.sub (fixes #170)
…inx-warning Fix Sphinx warning on idt_dna_sequence
…er and return description
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doc test failed even though docs compiled just fine locally. I suspect it is because the action we are using depends on an earlier version of Sphinx (2.4.4) When I run to installed that version, and run The action does not seem reliable as it has been more than a year since last update on the repo and it does not have a versioning to ensure stability going into the future. Probably time to revisit the doc check github action so that it doesn't rely on their action. In any case, I'm sure the action is failing due to a bug in their github action and not our docs |
dave-doty
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Let's not merge all of these changes yet. In particular, there are breaking changes with regard to removing pitch and yaw from Helix, and I want to make sure we are handling that properly both here and in the Dart code before merging into main.
Is there a way to include only the commit(s) involving changing the name of the main branch?
Also, it would be good to find a new way to have a GitHub Action that tests if the docs compile properly.
A hotfix branch could be made that merges directly to main containing just the change to the workflow. Alternatively, we can just wait since the only workflow that was affected is
Agreed, I will make an issue on this |
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scadnano PR v0.16.0 ready! |
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Can we try to fix the "Docs Check" action as part of this PR as well? I'd like to get that back to a state where it doesn't have a false alarm. (I haven't compiled the docs locally recently, so I don't even know whether the current alarm is false, but the check is not passing.) |
Ok, I'll look into it |
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@dave-doty While working on docs check workflow, I found that you can subscribe to notifications on the ReadTheDocs project site so that you get notified via email if a build fails. I'm still going to try to add a workflow to do the doc check, but thought this is good to know |
Merged from PR #178 * Update docs-check.yml * Fix typo: "docs" -> "doc" * Move "make html" to same shell as "cd" command * Use sphinx-build command with -W flag This makes it so that warnings are treated as errors (consistent with Read the Docs)
dave-doty
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Can you please add to the release notes that there is a breaking change?
It would also be good to document this change: fixes #168: ensure grid fields are of type Grid, not str or None, since it might break existing code that was manually passing in strings for the grid parameter.
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