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{"action":"created","issue":{"url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21","repository_url":"https://api.github.com/repos/kalekundert/autoclasstoc","labels_url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21/comments","events_url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21/events","html_url":"https://github.com/kalekundert/autoclasstoc/issues/21","id":1264723015,"node_id":"I_kwDOD6ti9M5LYiRH","number":21,"title":"Error when module's qualified name is different from the module file location","user":{"login":"whitews","id":1298022,"node_id":"MDQ6VXNlcjEyOTgwMjI=","avatar_url":"https://avatars.githubusercontent.com/u/1298022?v=4","gravatar_id":"","url":"https://api.github.com/users/whitews","html_url":"https://github.com/whitews","followers_url":"https://api.github.com/users/whitews/followers","following_url":"https://api.github.com/users/whitews/following{/other_user}","gists_url":"https://api.github.com/users/whitews/gists{/gist_id}","starred_url":"https://api.github.com/users/whitews/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whitews/subscriptions","organizations_url":"https://api.github.com/users/whitews/orgs","repos_url":"https://api.github.com/users/whitews/repos","events_url":"https://api.github.com/users/whitews/events{/privacy}","received_events_url":"https://api.github.com/users/whitews/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2022-06-08T13:08:27Z","updated_at":"2022-06-08T15:20:13Z","closed_at":null,"author_association":"NONE","active_lock_reason":null,"body":"Hi Kale,\r\n\r\nThanks for your work on this project, I find it very useful for documenting large classes.\r\n\r\nI have a [project](https://github.com/whitews/FlowKit) where, via `__init__` files, the qualified names differ from the file path for files containing some class definitions. When I try to add `.. autoclasstoc::` to an existing RST doc (that successfully builds prior to adding), I get a `ModuleNotFound` error. For example, I have a `RectangleGate` class that has the qualified path `flowkit.gates.RectangleGate` and would be imported like:\r\n\r\n`from flowkit.gates import RectangleGate`\r\n\r\nbut the actual file path to the module where the class is defined is:\r\n\r\n`flowkit/_models/gates/_gates.py`\r\n\r\nThis was a working docs build prior to adding the autoclasstoc line for this class. The RST file that triggers the error:\r\n\r\n```\r\nRectangleGate Class\r\n===================\r\n\r\n.. currentmodule:: flowkit.gates\r\n\r\n.. autoclass:: RectangleGate\r\n :members:\r\n\r\n .. autoclasstoc::\r\n```\r\n\r\nFull stack trace:\r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/cmd/build.py\", line 276, in build_main\r\n app.build(args.force_all, filenames)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/application.py\", line 329, in build\r\n self.builder.build_update()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/builders/__init__.py\", line 288, in build_update\r\n self.build(to_build,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/builders/__init__.py\", line 302, in build\r\n updated_docnames = set(self.read())\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/builders/__init__.py\", line 409, in read\r\n self._read_serial(docnames)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/builders/__init__.py\", line 430, in _read_serial\r\n self.read_doc(docname)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/builders/__init__.py\", line 483, in read_doc\r\n publisher.publish()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/core.py\", line 217, in publish\r\n self.document = self.reader.read(self.source, self.parser,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/io.py\", line 103, in read\r\n self.parse()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/readers/__init__.py\", line 78, in parse\r\n self.parser.parse(self.input, document)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/parsers.py\", line 78, in parse\r\n self.statemachine.run(inputlines, document, inliner=self.inliner)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 170, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2779, in underline\r\n self.section(title, source, style, lineno - 1, messages)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 327, in section\r\n self.new_subsection(title, lineno, messages)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 393, in new_subsection\r\n newabsoffset = self.nested_parse(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 281, in nested_parse\r\n state_machine.run(block, input_offset, memo=self.memo,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 196, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2354, in explicit_markup\r\n self.explicit_list(blank_finish)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2379, in explicit_list\r\n newline_offset, blank_finish = self.nested_list_parse(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 318, in nested_list_parse\r\n state_machine.run(block, input_offset, memo=self.memo,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 196, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2354, in explicit_markup\r\n self.explicit_list(blank_finish)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2379, in explicit_list\r\n newline_offset, blank_finish = self.nested_list_parse(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 318, in nested_list_parse\r\n state_machine.run(block, input_offset, memo=self.memo,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 196, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2657, in explicit_markup\r\n nodelist, blank_finish = self.explicit_construct(match)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2364, in explicit_construct\r\n return method(self, expmatch)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2101, in directive\r\n return self.run_directive(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2151, in run_directive\r\n result = directive_instance.run()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/ext/autodoc/directive.py\", line 159, in run\r\n result = parse_generated_content(self.state, params.result, documenter)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/ext/autodoc/directive.py\", line 106, in parse_generated_content\r\n state.nested_parse(content, 0, node)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 281, in nested_parse\r\n state_machine.run(block, input_offset, memo=self.memo,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 196, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2352, in explicit_markup\r\n nodelist, blank_finish = self.explicit_construct(match)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2364, in explicit_construct\r\n return method(self, expmatch)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2101, in directive\r\n return self.run_directive(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2151, in run_directive\r\n result = directive_instance.run()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/domains/__init__.py\", line 281, in run\r\n return super().run()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/sphinx/directives/__init__.py\", line 199, in run\r\n self.state.nested_parse(self.content, self.content_offset, contentnode)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 281, in nested_parse\r\n state_machine.run(block, input_offset, memo=self.memo,\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 196, in run\r\n results = StateMachineWS.run(self, input_lines, input_offset)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 240, in run\r\n context, next_state, result = self.check_line(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/statemachine.py\", line 452, in check_line\r\n return method(match, context, next_state)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2352, in explicit_markup\r\n nodelist, blank_finish = self.explicit_construct(match)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2364, in explicit_construct\r\n return method(self, expmatch)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2101, in directive\r\n return self.run_directive(\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/docutils/parsers/rst/states.py\", line 2151, in run_directive\r\n result = directive_instance.run()\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/autoclasstoc/plugin.py\", line 29, in run\r\n mod, cls = utils.load_class(mod_name, cls_name)\r\n File \"../envs/flowkit-dev/lib/python3.10/site-packages/autoclasstoc/utils.py\", line 46, in load_class\r\n mod = import_module(mod_name)\r\n File \"/usr/lib/python3.10/importlib/__init__.py\", line 126, in import_module\r\n return _bootstrap._gcd_import(name[level:], package, level)\r\n File \"<frozen importlib._bootstrap>\", line 1050, in _gcd_import\r\n File \"<frozen importlib._bootstrap>\", line 1027, in _find_and_load\r\n File \"<frozen importlib._bootstrap>\", line 1004, in _find_and_load_unlocked\r\nModuleNotFoundError: No module named 'flowkit.gates'\r\n```\r\n","reactions":{"url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21/timeline","performed_via_github_app":null,"state_reason":null},"comment":{"url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/comments/1150060500","html_url":"https://github.com/kalekundert/autoclasstoc/issues/21#issuecomment-1150060500","issue_url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/21","id":1150060500,"node_id":"IC_kwDOD6ti9M5EjIfU","user":{"login":"kalekundert","id":298132,"node_id":"MDQ6VXNlcjI5ODEzMg==","avatar_url":"https://avatars.githubusercontent.com/u/298132?v=4","gravatar_id":"","url":"https://api.github.com/users/kalekundert","html_url":"https://github.com/kalekundert","followers_url":"https://api.github.com/users/kalekundert/followers","following_url":"https://api.github.com/users/kalekundert/following{/other_user}","gists_url":"https://api.github.com/users/kalekundert/gists{/gist_id}","starred_url":"https://api.github.com/users/kalekundert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kalekundert/subscriptions","organizations_url":"https://api.github.com/users/kalekundert/orgs","repos_url":"https://api.github.com/users/kalekundert/repos","events_url":"https://api.github.com/users/kalekundert/events{/privacy}","received_events_url":"https://api.github.com/users/kalekundert/received_events","type":"User","site_admin":false},"created_at":"2022-06-08T15:20:13Z","updated_at":"2022-06-08T15:20:13Z","author_association":"OWNER","body":"Thanks for the bug report. I'm not immediately sure what's causing the problem, since it seems like the code already trying to do the right thing: import `flowkit.gates` via `importlib.import_module` (which should behave identically to `import flowkit.gates`).\r\n\r\nCan you double-check that `sys.path` is set correctly? I found the FlowKit github repo and took a look at `conf.py`. The ` sys.path.insert(0, os.path.abspath('../..'))` approach is fragile, since it's relative to the directory that sphinx is invoked from. Better would be to (i) install `flowkit` using pip and not change `sys.path` at all or (ii) configure `sys.path` relative to `__file__`, e.g. `sys.path.insert(os.path.dirname(os.path.dirname(__file__)))` or similar.\r\n\r\nLet me know if either of those approaches solve the problem, otherwise I'll look into this more over the weekend.\r\n\r\n---\r\n\r\nCompletely unrelated to this issue, I have a library that I use for flow cytometry analysis that I want to ~~shamelessly plug~~bring to your attention, since it seems complementary to FlowKit and might be useful to you. It's called [wellmap](https://wellmap.readthedocs.io/en/latest/), and it's basically a simple text file format that allows you to describe which experimental conditions are tested in which wells of a microplate. It's very useful for writing analysis scripts (such as those using FlowKit) that aren't tied to one specific plate layout.","reactions":{"url":"https://api.github.com/repos/kalekundert/autoclasstoc/issues/comments/1150060500/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"performed_via_github_app":null}}
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