remove quarto dep, fix docs

Author: kenjimarshall

README.md

@@ -1,6 +1,6 @@
 # BIL Data Python API
 
-This repository contains the public-facing Python API for accessing and analyzing neural data from the [Brain Interfacing Laboratory](https://bil.stanford.edu/). The public deposition is at the [Stanford Digital Repository (SDR)](https://purl.stanford.edu/zz618yg1930).
+This is a Python API for accessing and analyzing neural data from the [Brain Interfacing Laboratory](https://bil.stanford.edu/). The public deposition is at the [Stanford Digital Repository (SDR)](https://purl.stanford.edu/zz618yg1930).
 
 ## Installation
 
@@ -10,11 +10,9 @@ pip install bilab
 
 ## Data Availability
 
-The `bil` package is an API for interacting with [publicly deposited data](https://purl.stanford.edu/zz618yg1930). In that directory, each recording session has its own identifier under the `data` directory. For instance, "U201130_01" is the first session by subject U on 2020-11-30.
+The `bilab` package is an API for interacting with [publicly deposited data](https://purl.stanford.edu/zz618yg1930). In that directory, each recording session has its own identifier under the `data` directory. For instance, "U201130_01" is the first session by subject U on 2020-11-30.
 
-**Not all data types are available for all sessions.**
-
-Public datasets are deposited incrementally. The API contains methods for signals that will raise a `FileNotFoundError` if those signals have not been published.
+This is a public distribution of an internal API, and **not all data types are publicly available for all sessions.** Public datasets are deposited incrementally. The API contains methods for signals that will raise a `FileNotFoundError` if those signals have not been published. The deposition is growing incrementally to permit reproduction and extension upon published results.
 
 ## Quickstart
 
@@ -40,22 +38,6 @@ span = study.spans[0]
 lfp = span.lfp(region="m1")  # (96, T) ndarray
 ```
 
-## Development
-
-For development, clone the repository and install the additional `dev` dependencies:
-
-```bash
-pip install -e ".[dev]"
-```
-
-Alternatively, `uv` can be used to pull the latest `uv.lock` into a virtual environment:
+## Contributing
 
-```bash
-uv sync --all-extras
-```
-
-Finally, configure pre-commit hooks:
-
-```bash
-pre-commit install
-```
+This is a public distribution of an internal API; at this time, development is proceeding internally.

docs/quickstart.ipynb

@@ -19,14 +19,8 @@
    "source": [
     "First, install the package!\n",
     "\n",
-    "**Via HTTPS:**\n",
     "```bash\n",
-    "pip install git+https://github.com/bil/data-python.git\n",
-    "```\n",
-    "\n",
-    "**Via SSH:**\n",
-    "```bash\n",
-    "pip install git+ssh://git@github.com/bil/data-python.git\n",
+    "pip install bilab\n",
     "```"
    ]
   },
@@ -38,7 +32,7 @@
     "## Data Availability Disclaimer\n",
     "\n",
     "1. **Incremental Releases:** The public deposition in the [SDR](https://purl.stanford.edu/zz618yg1930) is being expanded incrementally and only contains data associated with formal publications.\n",
-    "2. **Missing Files:** Because of this, many API methods **will not work** until the corresponding data has been released. These will fail with a `FileNotFoundError`."
+    "2. **Missing Files:** Because of this, many API methods targetting unpublished data **will not work** until the corresponding data has been released, and will raise a `FileNotFoundError`."
    ]
   },
   {
@@ -382,7 +376,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bilab"
-version = "0.1.2"
+version = "0.1.4"
 description = "A data API for the Brain Interfacing Laboratory"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -38,7 +38,6 @@ Repository = "https://github.com/bil/data-python"
 
 [project.optional-dependencies]
 dev = [
-    "quarto-cli",
     "pytest",
     "pytest-mock",
     "nbstripout",

scripts/release.sh

@@ -4,10 +4,18 @@ if [[ -n "$(git status --porcelain)" ]] then
     echo "Nonempty status"
     exit 1
 fi
-# Run AFTER bumping version
-git tag "v$(uv version --short)"
-git push --tags
+if [[ ! -f .env ]] then
+    echo "Missing .env"
+    exit 1
+fi
+# push commits
+git push origin HEAD:main
+# tag commit
+tag="v$(uv version --short)"
+git tag "$tag"
+# push tag
+git push github $tag
 # Expect PYPI_TOKEN in a .env
-[ ! -f .env ] || export $(grep -v '^#' .env | xargs)
+source .env
 uv build
 uv publish --token $PYPI_TOKEN