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drammockdrammock
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fix everything
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‎doc/install/mne_tools_suite.rst‎

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Overview of the MNE tools suite
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===============================
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tak
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MNE-Python is an open-source Python module for processing, analysis, and
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visualization of functional neuroimaging data (EEG, MEG, sEEG, ECoG, and
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fNIRS). There are several related or interoperable software packages that you

‎doc/sphinxext/related_software.py‎

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@@ -116,8 +116,9 @@ def _get_mapping(packages):
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mapping = dict()
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for line in (txt.read_text() + "\n" + txt_nodeps.read_text()).split("\n"):
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line = line.strip()
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if not line or line.startswith("#"):
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if not line or line.startswith("##"):
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continue
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line = line.lstrip("# ")
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pkg = line.split("#")[0].strip()
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# just keep anything after "categories: " to end of line
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if "categories: " in line:
@@ -127,18 +128,19 @@ def _get_mapping(packages):
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# split the comma-separated list of categories into a tuple of strings
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mapping[pkg] = tuple([x.strip() for x in categories.split(",")])
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# unpack the tuples to make a single sequence of (unique) categories
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cats = sorted(set([cat for cats in mapping.values() for cat in cats]))
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categories = sorted(set([cat for cats in mapping.values() for cat in cats]))
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# put "other" last
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if "Other" in cats:
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cats.remove("Other")
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cats.append("Other")
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if "Other" in categories:
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categories.remove("Other")
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categories.append("Other")
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# now, invert the mapping to be category: list of packages
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rev_mapping = dict()
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for cat in cats:
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for cat in categories:
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rev_mapping[cat] = tuple([pkg for pkg, cats in mapping.items() if cat in cats])
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# extra packages: not in the two text files
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extras = tuple(set(packages) - set(mapping))
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rev_mapping["Other"] = tuple(sorted(rev_mapping.get("Other", ()) + extras))
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if len(other := tuple(sorted(rev_mapping.get("Other", ()) + extras))):
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rev_mapping["Other"] = other
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return rev_mapping
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@@ -247,8 +249,6 @@ def run(self):
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for package in packages:
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data = pkg_data.get(package.lower(), {})
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if not data:
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print(package)
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item = nodes.list_item()
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if "description" not in data:
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para = nodes.paragraph(text=f"{package}")

‎doc/sphinxext/related_software.txt‎

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Original file line numberDiff line numberDiff line change
@@ -1,29 +1,28 @@
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# This file is used to install extra packages into CircleCI when building our docs.
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# The purpose is to allow the packages in the "related software" list to be introspected
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# so we can get their URLs and Summary descriptions automatically.
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# Related software with onerous dependencies (e.g., torch and tensorflow)
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# should be added to `related_software_nodeps.txt` instead.
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# Ideally each package should be tagged as one or more of the following categories;
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# packages with no tags will be categorized as "Other".
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# Make sure to put categories at the END of the line, separated by commas if a package
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# fits in multiple categories.
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#
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# LIST OF CATEGORIES
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# ==================
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# Connectivity and source analysis
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# Data I/O and interoperability
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# Data organization and workflows
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# Microstates and neural states
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# Oscillations and time-frequency analysis
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# Other physiological signals and modalities
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# Preprocessing and artifact correction
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# Statistics and machine learning
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# Visualization and real-time analysis
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#
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# MNE-PYTHON OPTIONAL DEPENDENCIES THAT WE ALSO WANT IN THE CATEGORIZED LIST
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# ==========================================================================
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## This file is used to install extra packages into CircleCI when building our docs.
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## The purpose is to allow the packages in the "related software" list to be introspected
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## so we can get their URLs and Summary descriptions automatically.
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## Related software with onerous dependencies (e.g., torch and tensorflow)
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## should be added to `related_software_nodeps.txt` instead.
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## Ideally each package should be tagged as one or more of the following categories;
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## packages with no tags will be categorized as "Other".
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## Make sure to put categories at the END of the line, separated by commas if a package
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## fits in multiple categories.
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##
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## LIST OF CATEGORIES
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## ==================
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## Connectivity and source analysis
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## Data I/O and interoperability
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## Data organization and workflows
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## Microstates and neural states
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## Oscillations and time-frequency analysis
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## Other physiological signals and modalities
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## Preprocessing and artifact correction
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## Statistics and machine learning
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## Visualization and real-time analysis
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##
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## MNE-PYTHON OPTIONAL DEPENDENCIES THAT WE ALSO WANT IN THE CATEGORIZED LIST
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## ==========================================================================
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# antio # categories: Data I/O and interoperability
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# best-python # categories: Data I/O and interoperability
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# dipy # categories: Other physiological signals and modalities
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# edfio # categories: Data I/O and interoperability
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# eeglabio # categories: Data I/O and interoperability
@@ -35,14 +34,21 @@
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# nilearn # categories: Statistics and machine learning, Other physiological signals and modalities
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# openmeeg # categories: Connectivity and source analysis
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# openneuro-py # categories: Data I/O and interoperability
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# posthoc # categories: Statistics and machine learning
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# pybv # categories: Data I/O and interoperability
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# snirf # categories: Other physiological signals and modalities
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##
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## PACKAGES THAT CAN'T BE PIP-INSTALLED FOR VARIOUS REASONS
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## ========================================================
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# best-python # categories: Data I/O and interoperability
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# conpy # categories: Connectivity and source analysis
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# eelbrain # categories: Statistics and machine learning, Visualization and real-time analysis
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# mne-hcp # categories: Data I/O and interoperability
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# posthoc # categories: Statistics and machine learning
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# surfa # categories: Visualization and real-time analysis, Other physiological signals and modalities
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#
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# ONES WE ACTUALLY NEED CIRCLECI TO INSTALL
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# =========================================
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alphaCSC # categories: Statistics and machine learning, Oscillations and time-frequency analysis
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##
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## ONES WE ACTUALLY NEED CIRCLECI TO INSTALL
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## =========================================
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alphacsc # categories: Statistics and machine learning, Oscillations and time-frequency analysis
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autoreject # categories: Preprocessing and artifact correction
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bycycle # categories: Oscillations and time-frequency analysis
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curryreader # categories: Data I/O and interoperability

‎doc/sphinxext/related_software_nodeps.txt‎

Lines changed: 9 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,13 @@
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# This file is used to install extra packages into CircleCI when building our docs.
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# The purpose is to allow the packages in the "related software" list to be introspected
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# so we can get their URLs and Summary descriptions automatically.
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# **This file** is for packages with onerous dependencies (e.g., torch and tensorflow);
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# the sibling file `related_software.txt` is for ordinary packages.
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# Ideally each package should be tagged as one or more of the categories shown at the
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# top of `related_software.txt`; packages with no tags will be categorized as "Other".
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# Make sure to put categories at the END of the line, separated by commas if a package
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# fits in multiple categories.
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conpy # requires future and subprocess32, which don't have wheels # categories: Connectivity and source analysis
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## This file is used to install extra packages into CircleCI when building our docs.
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## The purpose is to allow the packages in the "related software" list to be introspected
3+
## so we can get their URLs and Summary descriptions automatically.
4+
## **This file** is for packages with onerous dependencies (e.g., torch and tensorflow);
5+
## the sibling file `related_software.txt` is for ordinary packages.
6+
## Ideally each package should be tagged as one or more of the categories shown at the
7+
## top of `related_software.txt`; packages with no tags will be categorized as "Other".
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## Make sure to put categories at the END of the line, separated by commas if a package
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## fits in multiple categories.
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cross-domain-saliency-maps # tensorflow # categories: Statistics and machine learning
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eelbrain #nowheels # categories: Statistics and machine learning, Visualization and real-time analysis
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fsleyes # wxPython # categories: Other physiological signals and modalities, Visualization and real-time analysis
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mne-kit-gui # mayavi # categories: Preprocessing and artifact correction
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mne-videobrowser # opencv # categories: Visualization and real-time analysis

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