umbrella docs

.github/workflows/publish.yaml

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+name: Publish docs to GitHub pages 
+on:
+  push:
+    branches:
+      - master 
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material 
+      - run: mkdocs gh-deploy --force

CNAME

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+docs.bedbase.org

docs/bbconf/README.md

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+# bbconf
+
+`bbconf` defines `BedBaseConf` class which is an in-memory representation of the configuration file for the *BEDBASE* project. This is the source of the project-wide constant variables. Additionally it implements multiple convenience methods for interacting with the database backend, i.e. [PostgreSQL](https://www.postgresql.org/)

docs/bbconf/bbc_api.md

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+Final targets: BedBaseConf, get_bedbase_cfg
+<script>
+document.addEventListener('DOMContentLoaded', (event) => {
+  document.querySelectorAll('h3 code').forEach((block) => {
+    hljs.highlightBlock(block);
+  });
+});
+</script>
+
+<style>
+h3 .content { 
+    padding-left: 22px;
+    text-indent: -15px;
+ }
+h3 .hljs .content {
+    padding-left: 20px;
+    margin-left: 0px;
+    text-indent: -15px;
+    martin-bottom: 0px;
+}
+h4 .content, table .content, p .content, li .content { margin-left: 30px; }
+h4 .content { 
+    font-style: italic;
+    font-size: 1em;
+    margin-bottom: 0px;
+}
+
+</style>
+
+
+# Package `bbconf` Documentation
+
+## <a name="BedBaseConf"></a> Class `BedBaseConf`
+This class standardizes reporting of bedstat and bedbuncher results. It formalizes a way for these pipelines and downstream tools to communicate -- the produced results can easily and reliably become an input for the server. The object exposes API for interacting with the results and is backed by a [PostgreSQL](https://www.postgresql.org/) database.
+
+
+```python
+def __init__(self, config_path=None, database_only=False)
+```
+
+Initialize the object
+#### Parameters:
+
+- `config_path` (`str`):  path to the bedbase configuration file
+- `database_only` (`bool`):  whether the database managers should notkeep an in-memory copy of the data in the database
+
+
+
+
+```python
+def bed(self)
+```
+
+PipestatManager of the bedfiles table
+#### Returns:
+
+- `pipestat.PipestatManager`:  manager of the bedfiles table
+
+
+
+
+```python
+def bedset(self)
+```
+
+PipestatManager of the bedsets table
+#### Returns:
+
+- `pipestat.PipestatManager`:  manager of the bedsets table
+
+
+
+
+```python
+def config(self)
+```
+
+Config used to initialize the object
+#### Returns:
+
+- `yacman.YacAttMap`:  bedbase configuration file contents
+
+
+
+
+```python
+def get_bedbuncher_output_path(self, remote=False)
+```
+
+Get path to the output of the bedbuncher pipeline
+#### Parameters:
+
+- `remote` (`bool`):  whether to use remote url base
+
+
+#### Returns:
+
+- `str`:  path to the bedbuncher pipeline output
+
+
+
+
+```python
+def get_bedstat_output_path(self, remote=False)
+```
+
+Get path to the output of the bedstat pipeline
+#### Parameters:
+
+- `remote` (`bool`):  whether to use remote url base
+
+
+#### Returns:
+
+- `str`:  path to the bedstat pipeline output
+
+
+
+
+```python
+def remove_relationship(self, bedset_id, bedfile_ids=None)
+```
+
+Remove entries from the relationships table
+#### Parameters:
+
+- `bedset_id` (`str`):  id of the bedset to remove
+- `bedfile_ids` (`list[str]`):  ids of the bedfiles to remove for theselected bedset. If none provided, all the relationsips for the selected bedset will be removed.
+
+
+
+
+```python
+def report_relationship(self, bedset_id, bedfile_id)
+```
+
+Report a bedfile for bedset.
+
+Inserts the ID pair into the relationship table, which allows to
+manage many to many bedfile bedset relationships
+#### Parameters:
+
+- `bedset_id` (`int`):  id of the bedset to report bedfile for
+- `bedfile_id` (`int`):  id of the bedfile to report
+
+
+
+
+```python
+def select_bedfiles_for_bedset(self, condition=None, condition_val=None, bedfile_col=None)
+```
+
+Select bedfiles that are part of a bedset that matches the query
+#### Parameters:
+
+- `condition` (`str`):  bedsets table query to restrict the results with,for instance `"id=%s"`
+- `condition_val` (`list[str]`):  values to populate the condition stringwith
+- `bedfile_col` (`list[str] | str`):  bedfile columns to include in theresult, if none specified all columns will be included
+
+
+#### Returns:
+
+- `list[psycopg2.extras.DictRow]`:  matched bedfiles table contents
+
+
+
+
+```python
+def get_bedbase_cfg(cfg=None)
+```
+
+Determine path to the bedbase configuration file
+
+The path can be either explicitly provided
+or read from a $BEDBASE environment variable
+#### Parameters:
+
+- `cfg` (`str`):  path to the config file.Optional, the $BEDBASE config env var will be used if not provided
+
+
+#### Returns:
+
+- `str`:  configuration file path
+
+
+
+
+
+
+
+*Version Information: `bbconf` v0.1.0, generated by `lucidoc` v0.4.3*

docs/bbconf/changelog.md

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+# Changelog
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+
+## [0.4.0] - 2023-10-17
+### Change
+- bbconf to use pipestat v0.4.1 and SQLModel
+- Added qdrant search, and insert methods
+- Fixed tests
+
+## [0.3.0] - 2022-08-18
+### Change
+- update select_bedfiles_for_distance
+- update database table schema
+
+## [0.2.1] - 2021-11-11
+### Fix
+- attempt to fix database connection error
+
+## [0.2.0] - 2021-10-25
+**This release introduces backwards incompatible changes** 
+### Changed
+- switched to object-relational mapping approach (ORM) for database interface
+
+
+## [0.1.1] - 2021-04-15
+### Added
+- added new fields in the bedfiles and bedsets schema
+
+## [0.1.0] - 2021-02-22
+**This release introduces backwards incompatible changes**
+### Changed
+- `BedBaseConf` backend (database) to [PostgreSQL](https://www.postgresql.org/)
+- complete `BedBaseConf` class redesign
+
+## [0.0.2] - 2020-05-28
+### Added
+- index deleting methods:
+	- `delete_bedsets_index`
+	- `delete_bedfiles_index`
+- multiple new keys constants
+
+### Changed
+- make `search_bedfiles` and `search_bedsets` methods return all hits by default instead of just 10. Parametrize it.
+- added more arguments to `insert_bedfiles_data` and `insert_bedsets_data` method interfaces: `doc_id` and `force_update`
+- Elasticsearch documents are inserted into the indices more securily, `insert_*` methods prevent documents duplication
+
+
+## [0.0.1] - 2020-02-05
+### Added
+- initial project release