Final tweaks/handle merge

GenomicMedLab · Mar 19, 2024 · 64bccb2 · 64bccb2
1 parent 2072fb1
commit 64bccb2
Show file tree

Hide file tree

Showing 26 changed files with 58 additions and 24 deletions.
diff --git a/docs/source/reference/api/handlers/wags_tails.utils.downloads.rst b/docs/source/reference/api/handlers/wags_tails.utils.downloads.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/handlers/wags_tails.utils.storage.rst b/docs/source/reference/api/handlers/wags_tails.utils.storage.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/handlers/wags_tails.utils.versioning.rst b/docs/source/reference/api/handlers/wags_tails.utils.versioning.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/sources/wags_tails.chembl.rst b/docs/source/reference/api/sources/wags_tails.chembl.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.chemidplus.rst b/docs/source/reference/api/sources/wags_tails.chemidplus.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.do.rst b/docs/source/reference/api/sources/wags_tails.do.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.drugbank.rst b/docs/source/reference/api/sources/wags_tails.drugbank.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.drugsatfda.rst b/docs/source/reference/api/sources/wags_tails.drugsatfda.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ensembl.rst b/docs/source/reference/api/sources/wags_tails.ensembl.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ensembl_transcript_mappings.rst b/docs/source/reference/api/sources/wags_tails.ensembl_transcript_mappings.rst
@@ -0,0 +1,9 @@
+wags_tails.ensembl_transcript_mappings
+======================================
+
+.. automodule:: wags_tails.ensembl_transcript_mappings
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :inherited-members:
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.guide_to_pharmacology.rst b/docs/source/reference/api/sources/wags_tails.guide_to_pharmacology.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.hemonc.rst b/docs/source/reference/api/sources/wags_tails.hemonc.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.hgnc.rst b/docs/source/reference/api/sources/wags_tails.hgnc.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.mondo.rst b/docs/source/reference/api/sources/wags_tails.mondo.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ncbi.rst b/docs/source/reference/api/sources/wags_tails.ncbi.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ncbi_lrg_refseqgene.rst b/docs/source/reference/api/sources/wags_tails.ncbi_lrg_refseqgene.rst
@@ -0,0 +1,9 @@
+wags_tails.ncbi_lrg_refseqgene
+==============================
+
+.. automodule:: wags_tails.ncbi_lrg_refseqgene
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :inherited-members:
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ncbi_mane_summary.rst b/docs/source/reference/api/sources/wags_tails.ncbi_mane_summary.rst
@@ -0,0 +1,9 @@
+wags_tails.ncbi_mane_summary
+============================
+
+.. automodule:: wags_tails.ncbi_mane_summary
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :inherited-members:
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.ncit.rst b/docs/source/reference/api/sources/wags_tails.ncit.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.oncotree.rst b/docs/source/reference/api/sources/wags_tails.oncotree.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/sources/wags_tails.rxnorm.rst b/docs/source/reference/api/sources/wags_tails.rxnorm.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :inherited-members:
-   :exclude-members: model_fields, model_config, count, index
+   :exclude-members: model_fields, model_config, count, index
diff --git a/docs/source/reference/api/wags_tails.base_source.rst b/docs/source/reference/api/wags_tails.base_source.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :private-members:
-   :exclude-members: model_fields, model_config, _abc_impl
+   :exclude-members: model_fields, model_config, _abc_impl
diff --git a/docs/source/reference/api/wags_tails.custom.rst b/docs/source/reference/api/wags_tails.custom.rst
@@ -6,4 +6,4 @@
    :undoc-members:
    :special-members: __init__
    :private-members:
-   :exclude-members: model_fields, model_config, _abc_impl
+   :exclude-members: model_fields, model_config, _abc_impl
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -32,11 +32,14 @@ Data Sources
    wags_tails.drugbank
    wags_tails.drugsatfda
    wags_tails.ensembl
+   wags_tails.ensembl_transcript_mappings
    wags_tails.guide_to_pharmacology
    wags_tails.hemonc
    wags_tails.hgnc
    wags_tails.mondo
    wags_tails.ncbi
+   wags_tails.ncbi_lrg_refseqgene
+   wags_tails.ncbi_mane_summary
    wags_tails.ncit
    wags_tails.oncotree
    wags_tails.rxnorm

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -8,7 +8,7 @@ Data source classes provide a :py:meth:`~wags_tails.base_source.DataSource.get_l
 .. code-block:: pycon
 
    >>> from wags_tails.mondo import MondoData
-   >>> m = MondoData()
+   >>> m = MondoData(silent=False)
    >>> m.get_latest(force_refresh=True)
    Downloading mondo.obo: 100%|█████████████████| 171M/171M [00:28<00:00, 6.23MB/s]
    PosixPath('/Users/genomicmedlab/.local/share/wags_tails/mondo/mondo_v2023-09-12.obo'), 'v2023-09-12'
@@ -28,7 +28,7 @@ Additional parameters are available to force usage of the most recent locally-av
 Configuration
 -------------
 
-All data is stored within source-specific subdirectories of a designated ``wags-tails`` data directory. By default, this location is ``~/.local/share/wags_tails/``, but it can be configured by passing a Path directly to a data class on initialization, via the ``$WAGS_TAILS_DIR`` environment variable, or via `XDG data environment variables <https://specifications.freedesktop.org/basedir-spec/basedir-spec-0.6.html>`_.
+All data is stored within source-specific subdirectories of a designated ``wags-tails`` data directory. By default, this location is ``~/.local/share/wags_tails/``, but it can be configured by passing a Path directly to a data class on initialization, via the ``$WAGS_TAILS_DIR`` environment variable, or via `XDG data environment variables <https://specifications.freedesktop.org/basedir-spec/basedir-spec-0.6.html>`_. This is explicated in full in the :py:meth:`~wags_tails.utils.storage.get_data_dir()` method description.
 
 .. _custom_data_source:
 
@@ -39,6 +39,10 @@ Custom Data Source
 
 .. code-block:: python
 
+   import datetime
+   from pathlib import Path
+   import json
+
    from wags_tails import CustomData, DataSource
    from wags_tails.utils.versioning import DATE_VERSION_PATTERN
    from wikibaseintegrator.wbi_helpers import execute_sparql_query

diff --git a/src/wags_tails/ensembl.py b/src/wags_tails/ensembl.py
@@ -8,7 +8,7 @@
 
 
 class EnsemblData(DataSource):
-    """Provide access to Ensembl data."""
+    """Provide access to Ensembl gene data."""
 
     _src_name = "ensembl"
     _filetype = "gff"

diff --git a/src/wags_tails/ncbi.py b/src/wags_tails/ncbi.py
@@ -1,4 +1,4 @@
-"""Provide data fetching for NCBI."""
+"""Provide data fetching for NCBI gene data sources."""
 import ftplib
 import logging
 import re
@@ -96,7 +96,7 @@ class NcbiGenePaths(NamedTuple):
 
 
 class NcbiGeneData(DataSource):
-    """Provide access to Guide to Pharmacology data."""
+    """Provide access to NCBI Gene data."""
 
     _src_name = "ncbi"
     _filetype = "tsv"