From 3f566f372ec0d87c9b1e6314ea4dea53c381f88c Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Thu, 3 Aug 2023 15:02:06 -0400 Subject: [PATCH 1/4] Update _config.yml --- documentation/CP-plugins-documentation/_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/documentation/CP-plugins-documentation/_config.yml b/documentation/CP-plugins-documentation/_config.yml index 702fc3aa..1c0723e5 100644 --- a/documentation/CP-plugins-documentation/_config.yml +++ b/documentation/CP-plugins-documentation/_config.yml @@ -17,8 +17,8 @@ execute: # Information about where the book exists on the web repository: url: https://github.com/cellprofiler/cellprofiler-plugins - branch: main # Which branch of the repository should be used when creating links (optional) - path_to_book: CP-plugins-documentation + branch: master # Which branch of the repository should be used when creating links (optional) + path_to_book: documentation/CP-plugins-documentation html: baseurl: cellprofiler.github.io From 3b303666c9da493c4d7f8f853a6c0a9a49f87119 Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Thu, 3 Aug 2023 15:04:17 -0400 Subject: [PATCH 2/4] Add issue for zsh in macs --- documentation/CP-plugins-documentation/using_plugins.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/documentation/CP-plugins-documentation/using_plugins.md b/documentation/CP-plugins-documentation/using_plugins.md index 9c05ecdb..6b3d271b 100644 --- a/documentation/CP-plugins-documentation/using_plugins.md +++ b/documentation/CP-plugins-documentation/using_plugins.md @@ -71,6 +71,8 @@ pip install -e .[FLAG] ``` e.g. To install Cellpose the pip install command would be `pip install -e .[cellpose]` +If using Mac and getting an error saying `zsh: no matches found: .[somepackage]`, put the dot and square brackets in single quotes, ie `pip install -e '.[cellpose]'` + 5. **Open and use CellProfiler.** Please note that plugins that have separate install flags may have conflicting dependencies so we recommend making a separate python environment in which to run separate installations. @@ -157,4 +159,4 @@ These are all the folders you need to copy over: 7. **Open and use CellProfiler.** When you try to run your plugin in your pipeline, if you have missed copying over any specific requirements, it will give you an error message that will tell you what dependency is missing in the terminal window that opens with CellProfiler on Windows machines. -This information is not available in Mac machines. \ No newline at end of file +This information is not available in Mac machines. From 308032c9bca48be14b8767f793040035e90b1b22 Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Fri, 4 Aug 2023 17:02:28 -0400 Subject: [PATCH 3/4] Update _toc.yml --- documentation/CP-plugins-documentation/_toc.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/documentation/CP-plugins-documentation/_toc.yml b/documentation/CP-plugins-documentation/_toc.yml index 9c508c45..1d50f4a2 100644 --- a/documentation/CP-plugins-documentation/_toc.yml +++ b/documentation/CP-plugins-documentation/_toc.yml @@ -6,11 +6,13 @@ parts: - caption: Overview chapters: - file: using_plugins - sections: - - file: RunCellpose - file: supported_plugins - file: unsupported_plugins - file: contributing_plugins - file: troubleshooting - file: citing - file: versions + +- caption: Extra information about specific plugins + chapters: + - file: RunCellPose From 5a4a2d475b1d88d3b0e852b04c6d03472d68369c Mon Sep 17 00:00:00 2001 From: Erin Weisbart <54687786+ErinWeisbart@users.noreply.github.com> Date: Mon, 7 Aug 2023 14:17:43 -0700 Subject: [PATCH 4/4] runcellpose capitalization --- documentation/CP-plugins-documentation/_toc.yml | 2 +- .../CP-plugins-documentation/{RunCellPose.md => runcellpose.md} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename documentation/CP-plugins-documentation/{RunCellPose.md => runcellpose.md} (100%) diff --git a/documentation/CP-plugins-documentation/_toc.yml b/documentation/CP-plugins-documentation/_toc.yml index 1d50f4a2..130d6329 100644 --- a/documentation/CP-plugins-documentation/_toc.yml +++ b/documentation/CP-plugins-documentation/_toc.yml @@ -15,4 +15,4 @@ parts: - caption: Extra information about specific plugins chapters: - - file: RunCellPose + - file: runcellpose diff --git a/documentation/CP-plugins-documentation/RunCellPose.md b/documentation/CP-plugins-documentation/runcellpose.md similarity index 100% rename from documentation/CP-plugins-documentation/RunCellPose.md rename to documentation/CP-plugins-documentation/runcellpose.md