docs: Update the build requirements

docs/acmg_seqvars_criteria.rst

@@ -709,7 +709,7 @@ An initial prediction is fist done using the general purpose pathogenicity predi
 
 Then, for splicing the following is done.
 
-- If a SpliceAI prediction is performed then it is interpreted according to :footsite:t:`walker:2023`.
+- If a SpliceAI prediction is performed then it is interpreted according to :footcite:t:`walker:2023`.
 
 The highest-scoring variant is used for the final prediction.
 

docs/doc_manual.rst

@@ -147,7 +147,7 @@ Clinical Significance
 This card shows the semi-automated pathogenicity prediction based on InterVar.
 Using the buttons on the left you can...
 - Hide/show the terse mode of ACMG criteria display.
-  On show this will provide you an overview of just the different criteria and their evidence level, on hide you will see the full display also providing a description on every ACMG criterion and how it should be used.
+On show this will provide you an overview of just the different criteria and their evidence level, on hide you will see the full display also providing a description on every ACMG criterion and how it should be used.
 - hide/show failed criteria (not set to "active" by the little switch displayed left to every criterion)
 
 Tipp: you can also see are brief description of every ACMG criterion in the terse mode when moving your curser of the little "i" in the upper right corner of every ACMG criterion box.

docs/doc_queries.rst

@@ -12,14 +12,36 @@ This section describes the queries that are supported by REEV.
 Genes
 -----
 
+Gene queries in REEV allow users to search by HGNC symbol or NCBI/ENSEMBL/HGNC ID. Examples of gene queries include:
+
+- `BRCA1`: Search by HGNC symbol.
+- `HGNC:1100`: This refers to the BRCA1 gene.
+- `7273`: This is the NCBI ID for the TTN gene.
+
 .. _doc_queries_seqvar:
 
 -----------------
 Sequence Variants
 -----------------
 
+Sequence variant queries in REEV can be provided in HGVS notation, gnomAD style, or SPDI-style. Examples include:
+
+Development Environment Examples:
+- `NM_007294.4(BRCA1):c.5123C>A`: HGVS transcript SNV.
+- `NM_000179.3:c.4082del`: HGVS transcript deletion.
+- `NC_000017.10:g.41197728G>T`: HGVS genomic SNV.
+- `GRCh37-chr17-41197751-G-T`: gnomAD style variant.
+- `NC_000017.11:43039470:G:A`: Canonical SPDI.
+
 .. _doc_queries_strucvar:
 
 -------------------
 Structural Variants
 -------------------
+
+Structural variant queries in REEV can be provided in various formats including ISCN notation, colon-separated, or hyphen-separated formats. Examples include:
+
+- `DEL:chr17:41176312:41277500`: Deletion on chromosome 17.
+- `DUP-chrX-73565114-73956354`: Duplication on chromosome X.
+- `arr[GRCh37] 7q11(72,650,120_74,154,209)x1`: ISCN notation.
+- `GRCh37 7q11(72,650,120_74,154,209)x1`: Shorter form of ISCN notation.

docs/index.rst

@@ -50,6 +50,16 @@ It provides the following features as a central resource:
     doc_manual
     doc_clinvarsub
 
+.. toctree::
+    :hidden:
+    :maxdepth: 1
+    :caption: Contents
+
+    acmg_seqvars_criteria
+    acmg_seqvars_details
+    acmg_cnvs_criteria
+    acmg_cnvs_details
+
 .. toctree::
     :hidden:
     :maxdepth: 1

docs/requirements.txt

@@ -2,113 +2,208 @@ aiohttp==3.9.1
 aiosignal==1.3.1
 aiosqlite==0.19.0
 alabaster==0.7.13
-alembic==1.13.0
+alembic==1.13.1
+amqp==5.2.0
 annotated-types==0.6.0
-anyio==3.7.1
+anyio==4.2.0
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.3.0
+asgiref==3.7.2
+asttokens==2.4.1
+async-lru==2.0.4
 async-timeout==4.0.3
 asyncpg==0.29.0
-attrs==23.1.0
-Babel==2.13.1
-bcrypt==4.1.1
+attrs==23.2.0
+Babel==2.14.0
+bcrypt==4.1.2
 beautifulsoup4==4.12.2
-black==23.12.0
+billiard==4.2.0
+black==23.12.1
+bleach==6.1.0
 cachetools==5.3.2
+celery==5.3.6
+celery-types==0.20.0
 certifi==2023.11.17
 cffi==1.16.0
 chardet==5.2.0
 charset-normalizer==3.3.2
 click==8.1.7
+click-didyoumean==0.3.0
+click-plugins==1.1.1
+click-repl==0.3.0
+clinvar-this==0.14.6
 colorama==0.4.6
-coverage==7.3.2
+comm==0.2.0
+coverage==7.4.0
 cryptography==41.0.7
 cssselect==1.2.0
 cssutils==2.9.0
+debugpy==1.8.0
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+defusedxml==0.7.1
 dnspython==2.4.2
 docutils==0.20.1
 email-validator==2.0.0.post2
 emails==0.6
 exceptiongroup==1.2.0
-Faker==20.1.0
-fastapi==0.105.0
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 fastapi-users==12.1.2
 fastapi-users-db-sqlalchemy==6.0.1
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 frozenlist==1.4.0
 furo==2023.9.10
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+greenlet==3.0.3
 h11==0.14.0
-httpcore==0.17.3
-httpx
-httpx-oauth
+httpcore==1.0.2
+httpx==0.25.2
+httpx-oauth==0.13.1
 idna==3.6
 imagesize==1.4.1
 iniconfig==2.0.0
 install==1.3.5
-isort==5.13.1
+ipykernel==6.28.0
+ipython==8.19.0
+isoduration==20.11.0
+isort==5.13.2
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 Jinja2==3.1.2
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 latexcodec==2.0.1
 livereload==2.6.3
-lxml==4.9.3
+logzero==1.7.0
+lxml==5.0.0
 makefun==1.15.2
 Mako==1.3.0
 MarkupSafe==2.1.3
+matplotlib-inline==0.1.6
 mccabe==0.7.0
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 multidict==6.0.4
-mypy==1.7.1
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 mypy-extensions==1.0.0
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 packaging==23.2
+pandocfilters==1.5.0
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 passlib==1.7.4
 pathspec==0.12.1
+pexpect==4.9.0
 platformdirs==4.1.0
 pluggy==1.3.0
 premailer==3.10.0
+prometheus-client==0.19.0
+prompt-toolkit==3.0.43
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 psycopg2-binary==2.9.9
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+pure-eval==0.2.2
 pybtex==0.24.0
 pybtex-docutils==1.0.3
 pycodestyle==2.11.1
 pycparser==2.21
-pydantic==2.5.2
+pydantic==2.5.3
 pydantic-settings==2.1.0
-pydantic_core==2.14.5
+pydantic_core==2.14.6
 pyflakes==3.1.0
 Pygments==2.17.2
 PyJWT==2.8.0
-pytest==7.4.3
-pytest-asyncio==0.23.2
+pytest==7.4.4
+pytest-anyio==0.0.0
+pytest-asyncio==0.21.1
 pytest-cov==4.1.0
 pytest-faker==2.0.0
-pytest-httpx
+pytest-httpx==0.28.0
+pytest-mock==3.12.0
 pytest-subprocess==1.5.0
+pytest-xdist==3.5.0
 python-dateutil==2.8.2
 python-dotenv==1.0.0
+python-json-logger==2.0.7
 python-multipart==0.0.6
 PyYAML==6.0.1
+pyzmq==25.1.2
 redis==5.0.1
+referencing==0.32.0
 requests==2.31.0
 requests-mock==1.11.0
-sentry-sdk==1.38.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rpds-py==0.16.2
+Send2Trash==1.8.2
+sentry-sdk==1.39.1
 six==1.16.0
 sniffio==1.3.0
 snowballstemmer==2.2.0
 soupsieve==2.5
 Sphinx==7.2.6
 sphinx-autobuild==2021.3.14
 sphinx-basic-ng==1.0.0b2
+sphinx-rtd-theme==2.0.0
+sphinx-serve==1.0.1
 sphinxcontrib-applehelp==1.0.7
 sphinxcontrib-bibtex==2.6.1
 sphinxcontrib-devhelp==1.0.5
 sphinxcontrib-htmlhelp==2.0.4
+sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.6
 sphinxcontrib-serializinghtml==1.1.9
-SQLAlchemy==2.0.23
-starlette==0.27.0
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 tenacity==8.2.3
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+toml==0.10.2
 tomli==2.0.1
 tornado==6.4
+tqdm==4.66.1
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 types-passlib==1.7.7.13
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 types-requests==2.31.0.10
 typing_extensions==4.9.0
+tzdata==2023.4
+uri-template==1.3.0
 urllib3==2.1.0
-uvicorn==0.24.0.post1
+uvicorn==0.25.0
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 yarl==1.9.4
+zope.event==5.0
+zope.interface==6.1