eegdash 0.3.7.dev183881899__tar.gz → 0.3.9.dev114__tar.gz

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/MANIFEST.in

@@ -1,7 +1,7 @@
 include README.md
 include LICENSE
 
-include eegdash/dataset_summary.csv
+include eegdash/dataset/dataset_summary.csv
 
 recursive-include docs *.ipynb *.rst conf.py Makefile
 recursive-exclude docs *checkpoint.ipynb

{eegdash-0.3.7.dev183881899/eegdash.egg-info → eegdash-0.3.9.dev114}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.3.7.dev183881899
+Version: 0.3.9.dev114
 Summary: EEG data for machine learning
 Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License-Expression: GPL-3.0-only
@@ -40,6 +40,7 @@ Requires-Dist: h5io>=0.2.4
 Requires-Dist: pymatreader
 Requires-Dist: eeglabio
 Requires-Dist: tabulate
+Requires-Dist: docstring_inheritance
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -62,6 +63,7 @@ Requires-Dist: memory_profiler; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: lightgbm; extra == "docs"
 Requires-Dist: plotly; extra == "docs"
+Requires-Dist: nbformat; extra == "docs"
 Provides-Extra: all
 Requires-Dist: eegdash[docs]; extra == "all"
 Requires-Dist: eegdash[dev]; extra == "all"
@@ -106,7 +108,7 @@ EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine lea
 
 ## Data preprocessing
 
-EEGDash datasets are processed using the popular [BrainDecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are BrainDecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on BrainDecode datasets is also possible on EEGDash datasets. Refer to [BrainDecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
+EEGDash datasets are processed using the popular [braindecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are braindecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on braindecode datasets is also possible on EEGDash datasets. Refer to [braindecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
 
 ## EEG-Dash usage
 
@@ -129,7 +131,7 @@ ds_NDARDB033FW5 = EEGDashDataset(
 )
 ```
 
-This will search and download the metadata for the task **RestingState** for subject **NDARDB033FW5** in BIDS dataset **ds005514**. The actual data will not be downloaded at this stage. Following standard practice, data is only downloaded once it is processed. The **ds_NDARDB033FW5** object is a fully functional BrainDecode dataset, which is itself a PyTorch dataset. This [tutorial](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_eoec.ipynb) shows how to preprocess the EEG data, extracting portions of the data containing eyes-open and eyes-closed segments, then perform eyes-open vs. eyes-closed classification using a (shallow) deep-learning model. 
+This will search and download the metadata for the task **RestingState** for subject **NDARDB033FW5** in BIDS dataset **ds005514**. The actual data will not be downloaded at this stage. Following standard practice, data is only downloaded once it is processed. The **ds_NDARDB033FW5** object is a fully functional braindecode dataset, which is itself a PyTorch dataset. This [tutorial](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_eoec.ipynb) shows how to preprocess the EEG data, extracting portions of the data containing eyes-open and eyes-closed segments, then perform eyes-open vs. eyes-closed classification using a (shallow) deep-learning model. 
 
 To use the data from multiple subjects, enter:
 
@@ -145,7 +147,13 @@ This will search and download the metadata for the task 'RestingState' for all s
 
 ### Automatic caching
 
-EEGDash automatically caches the downloaded data in the .eegdash_cache folder of the current directory from which the script is called. This means that if you run the tutorial [scripts](https://github.com/sccn/EEGDash/tree/develop/notebooks), the data will only be downloaded the first time the script is executed.
+By default, EEGDash caches downloaded data under a single, consistent folder:
+
+- If ``EEGDASH_CACHE_DIR`` is set in your environment, that path is used.
+- Else, if MNE’s ``MNE_DATA`` config is set, that path is used to align with other EEG tooling.
+- Otherwise, ``.eegdash_cache`` in the current working directory is used.
+
+This means that if you run the tutorial [scripts](https://github.com/sccn/EEGDash/tree/develop/notebooks), the data will only be downloaded the first time the script is executed and reused thereafter.
 
 ## Education -- Coming soon...
 
@@ -159,4 +167,3 @@ EEG-DaSh is a collaborative initiative between the United States and Israel, sup
 
 
 
-

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/README.md

@@ -36,7 +36,7 @@ EEGDash queries return a **Pytorch Dataset** formatted to facilitate machine lea
 
 ## Data preprocessing
 
-EEGDash datasets are processed using the popular [BrainDecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are BrainDecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on BrainDecode datasets is also possible on EEGDash datasets. Refer to [BrainDecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
+EEGDash datasets are processed using the popular [braindecode](https://braindecode.org/stable/index.html) library. In fact, EEGDash datasets are braindecode datasets, which are themselves PyTorch datasets. This means that any preprocessing possible on braindecode datasets is also possible on EEGDash datasets. Refer to [braindecode](https://braindecode.org/stable/index.html) tutorials for guidance on preprocessing EEG data.
 
 ## EEG-Dash usage
 
@@ -59,7 +59,7 @@ ds_NDARDB033FW5 = EEGDashDataset(
 )
 ```
 
-This will search and download the metadata for the task **RestingState** for subject **NDARDB033FW5** in BIDS dataset **ds005514**. The actual data will not be downloaded at this stage. Following standard practice, data is only downloaded once it is processed. The **ds_NDARDB033FW5** object is a fully functional BrainDecode dataset, which is itself a PyTorch dataset. This [tutorial](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_eoec.ipynb) shows how to preprocess the EEG data, extracting portions of the data containing eyes-open and eyes-closed segments, then perform eyes-open vs. eyes-closed classification using a (shallow) deep-learning model. 
+This will search and download the metadata for the task **RestingState** for subject **NDARDB033FW5** in BIDS dataset **ds005514**. The actual data will not be downloaded at this stage. Following standard practice, data is only downloaded once it is processed. The **ds_NDARDB033FW5** object is a fully functional braindecode dataset, which is itself a PyTorch dataset. This [tutorial](https://github.com/sccn/EEGDash/blob/develop/notebooks/tutorial_eoec.ipynb) shows how to preprocess the EEG data, extracting portions of the data containing eyes-open and eyes-closed segments, then perform eyes-open vs. eyes-closed classification using a (shallow) deep-learning model. 
 
 To use the data from multiple subjects, enter:
 
@@ -75,7 +75,13 @@ This will search and download the metadata for the task 'RestingState' for all s
 
 ### Automatic caching
 
-EEGDash automatically caches the downloaded data in the .eegdash_cache folder of the current directory from which the script is called. This means that if you run the tutorial [scripts](https://github.com/sccn/EEGDash/tree/develop/notebooks), the data will only be downloaded the first time the script is executed.
+By default, EEGDash caches downloaded data under a single, consistent folder:
+
+- If ``EEGDASH_CACHE_DIR`` is set in your environment, that path is used.
+- Else, if MNE’s ``MNE_DATA`` config is set, that path is used to align with other EEG tooling.
+- Otherwise, ``.eegdash_cache`` in the current working directory is used.
+
+This means that if you run the tutorial [scripts](https://github.com/sccn/EEGDash/tree/develop/notebooks), the data will only be downloaded the first time the script is executed and reused thereafter.
 
 ## Education -- Coming soon...
 
@@ -89,4 +95,3 @@ EEG-DaSh is a collaborative initiative between the United States and Israel, sup
 
 
 
-

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/docs/Makefile

@@ -11,7 +11,7 @@ help:
 
 .PHONY: apidoc
 apidoc:
-	@sphinx-apidoc -o "$(APIDIR)" "../$(PKG)" -f -e -M
+	@python -m sphinx.ext.apidoc -o "$(APIDIR)" "../$(PKG)" -f -e -M
 
 # Standard build runs examples
 html: apidoc
@@ -28,4 +28,4 @@ Makefile: ;
 
 %: Makefile
 	@python prepare_summary_tables.py ../eegdash/ $(BUILDDIR)
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/docs/source/conf.py

@@ -1,4 +1,7 @@
+import importlib
+import inspect
 import os
+import sys
 from datetime import datetime, timezone
 
 from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
@@ -26,6 +29,7 @@ extensions = [
     "sphinx.ext.ifconfig",
     "sphinx.ext.intersphinx",
     "sphinx.ext.githubpages",
+    "sphinx.ext.linkcode",
     "sphinx.ext.napoleon",
     "sphinx_design",
     # "autoapi.extension",
@@ -55,7 +59,8 @@ html_baseurl = "https://sccn.github.io/eegdash/"
 
 html_theme_options = {
     "icon_links_label": "External Links",  # for screen reader
-    "use_edit_page_button": False,
+    # Show an "Edit this page" button linking to GitHub
+    "use_edit_page_button": True,
     "navigation_with_keys": False,
     "collapse_navigation": False,
     "header_links_before_dropdown": 6,
@@ -104,6 +109,69 @@ html_sidebars = {"api": [], "dataset_summary": [], "installation": []}
 # Copy extra files (e.g., robots.txt) to the output root
 html_extra_path = ["_extra"]
 
+# Provide GitHub context so the edit button and custom templates
+# (e.g., Sphinx-Gallery "Open in Colab") know where the source lives.
+# These values should match the repository and docs location.
+html_context = {
+    "github_user": "sccn",
+    "github_repo": "EEGDash",
+    # Branch used to build and host the docs
+    "github_version": "main",
+    # Path to the documentation root within the repo
+    "doc_path": "docs/source",
+}
+
+
+# Linkcode configuration: map documented objects to GitHub source lines
+def _linkcode_resolve_py_domain(info):
+    modname = info.get("module")
+    fullname = info.get("fullname")
+    if not modname:
+        return None
+
+    try:
+        submod = sys.modules.get(modname)
+        if submod is None:
+            submod = importlib.import_module(modname)
+
+        obj = submod
+        for part in fullname.split("."):
+            obj = getattr(obj, part)
+
+        # Unwrap decorators to reach the actual implementation
+        obj = inspect.unwrap(obj)
+        fn = inspect.getsourcefile(obj) or inspect.getfile(obj)
+        if not fn:
+            return None
+        fn = os.path.realpath(fn)
+
+        # Compute line numbers
+        try:
+            source, start = inspect.getsourcelines(obj)
+            end = start + len(source) - 1
+            linespec = f"#L{start}-L{end}"
+        except OSError:
+            linespec = ""
+
+        # Make path relative to repo root (parent of the installed package dir)
+        pkg_dir = os.path.realpath(os.path.dirname(eegdash.__file__))
+        repo_root = os.path.realpath(os.path.join(pkg_dir, os.pardir))
+        rel_path = os.path.relpath(fn, start=repo_root)
+
+        # Choose commit/branch for links; override via env if provided
+        commit = os.environ.get(
+            "LINKCODE_COMMIT", html_context.get("github_version", "main")
+        )
+        return f"https://github.com/{html_context['github_user']}/{html_context['github_repo']}/blob/{commit}/{rel_path}{linespec}"
+    except Exception:
+        return None
+
+
+def linkcode_resolve(domain, info):
+    if domain == "py":
+        return _linkcode_resolve_py_domain(info)
+    return None
+
 
 # -- Extension configurations ------------------------------------------------
 autoclass_content = "both"

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/docs/source/dataset_summary.rst

@@ -1,8 +1,7 @@
 .. meta::
    :hide_sidebar: true
-
-:html_theme.sidebar_secondary.remove:
-:html_theme.sidebar_primary.remove:
+   :html_theme.sidebar_secondary.remove: true
+   :html_theme.sidebar_primary.remove: true
 
 .. _data_summary:
 

{eegdash-0.3.7.dev183881899 → eegdash-0.3.9.dev114}/docs/source/index.rst

@@ -1,4 +1,5 @@
-:html_theme.sidebar_secondary.remove:
+.. meta::
+   :html_theme.sidebar_secondary.remove: true
 
 EEGDASH Documentation
 =====================
@@ -58,4 +59,3 @@ The archive is currently still in :bdg-danger:`beta testing` mode, so be kind.
    API <api/modules.rst>
    Dataset Summary <dataset_summary>
    Examples <generated/auto_examples/index>
-

eegdash-0.3.9.dev114/eegdash/__init__.py

@@ -0,0 +1,10 @@
+from .api import EEGDash, EEGDashDataset
+from .dataset import EEGChallengeDataset
+from .hbn import preprocessing
+from .utils import _init_mongo_client
+
+_init_mongo_client()
+
+__all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
+
+__version__ = "0.3.9.dev114"