feat: add counts to getModality and update docs for modality methods

jjjermiah · Mar 3, 2024 · 54874a3 · 54874a3
1 parent 1aa0ad1
commit 54874a3
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Showing 6 changed files with 23 additions and 8 deletions.
diff --git a/.gitignore b/.gitignore
@@ -157,3 +157,5 @@ src/nbiatoolkit/.DS_Store
 .vscode
 download.ipynb
 driver*.py
+logs
+logdir
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,7 @@ repos:
     rev: 22.10.0
     hooks:
     -   id: black
+
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
     hooks:

diff --git a/README.md b/README.md
@@ -85,10 +85,10 @@ For quick access to the NBIA, the toolkit also provides a command line interface
       /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
      / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
     /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/
-    
+
 Version: 0.33.0
 
-Available CLI tools: 
+Available CLI tools:
 
 getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
                [-o OUTPUTFILE] [--version]

diff --git a/docs/tutorial_files/2_ExploreCollections.rst b/docs/tutorial_files/2_ExploreCollections.rst
@@ -116,7 +116,7 @@ The :code:`Counts` parameter can be set to :code:`True` to return the number of
 
                with NBIAClient(return_type="dataframe") as client:
                   modalities = client.getModalityValues(
-                     collection = "TCGA-BLCA",
+                     Collection = "TCGA-BLCA",
                   )
 
                print(modalities)
@@ -131,8 +131,8 @@ The :code:`Counts` parameter can be set to :code:`True` to return the number of
 
                with NBIAClient(return_type="dataframe") as client:
                   modalities = client.getModalityValues(
-                     collection = "TCGA-BLCA",
-                     counts = True
+                     Collection = "TCGA-BLCA",
+                     Counts = True
                   )
 
                print(modalities)
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -16,7 +16,7 @@ getNewPatients = "nbiatoolkit.nbia_cli:getNewPatients_cli"
 getStudies = "nbiatoolkit.nbia_cli:getStudies_cli"
 getSeries = "nbiatoolkit.nbia_cli:getSeries_cli"
 getNewSeries = "nbiatoolkit.nbia_cli:getNewSeries_cli"
-# downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli"
+
 
 [tool.poetry.dependencies]
 python = ">=3.10 || 3.12"
@@ -34,6 +34,7 @@ jupyter = "^1.0.0"
 pytest-cov = ">=4.0.0"
 pytest-xdist = ">=3.5.0"
 mkdocs = "1.5.3"
+sphinx_exec_code = "0.12"
 myst-nb = {version = "^1.0.0", python = "^3.9"}
 sphinx-autoapi = "^3.0.0"
 sphinx-rtd-theme = "^1.3.0"