Merge pull request #233 from Project-MONAI/vikash/fixdocs

Fixed empty documentation on docs.monai

Author: gigony

docs/source/conf.py

@@ -16,7 +16,7 @@
 
     subprocess.call(
         "/bin/bash -c 'source /home/docs/checkouts/readthedocs.org/user_builds/"
-        f"{READTHEDOCS_PROJECT}/envs/{READTHEDOCS_VERSION}/bin/activate; ../../run setup'",
+        f"{READTHEDOCS_PROJECT}/envs/{READTHEDOCS_VERSION}/bin/activate; ../../run setup read_the_docs'",
         shell=True,
     )
     subprocess.call(

docs/source/index.md

@@ -7,5 +7,11 @@
 introduction/index
 getting_started/index
 developing_with_sdk/index
+```
+
+```{toctree}
+:glob:
+:maxdepth: 2
+
 modules/index
 ```

docs/source/modules/index.md

@@ -1,58 +1,14 @@
 # MODULES APIS
 
-## Core
-
 ```{toctree}
-:maxdepth: 3
-:hidden:
+:glob:
+:maxdepth: 2
 
 core
-```
-
-## Domain objects
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 domain_objects
-```
-
-## Operators
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 operators
-```
-
-## Models
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 models
-```
-
-## Graphs
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 graphs
-```
-
-## Executors
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 executors
-```
-
-## Datastores
-
-```{toctree}
-:maxdepth: 2
-:hidden:
 datastores
 ```

monai/deploy/cli/exec_command.py

@@ -24,7 +24,9 @@
 def create_exec_parser(subparser: _SubParsersAction, command: str, parents: List[ArgumentParser]) -> ArgumentParser:
     # Intentionally use `argparse.HelpFormatter` instead of `argparse.ArgumentDefaultsHelpFormatter`.
     # Default values for those options are None and those would be filled by `RuntimeEnv` object later.
-    parser = subparser.add_parser(command, formatter_class=argparse.HelpFormatter, parents=parents, add_help=False)
+    parser: ArgumentParser = subparser.add_parser(
+        command, formatter_class=argparse.HelpFormatter, parents=parents, add_help=False
+    )
 
     parser.add_argument("--input", "-i", help="Path to input folder/file (default: input)")
     parser.add_argument("--output", "-o", help="Path to output folder (default: output)")

monai/deploy/packager/package_command.py

@@ -17,7 +17,9 @@
 
 
 def create_package_parser(subparser: _SubParsersAction, command: str, parents: List[ArgumentParser]) -> ArgumentParser:
-    parser = subparser.add_parser(command, formatter_class=argparse.HelpFormatter, parents=parents, add_help=False)
+    parser: ArgumentParser = subparser.add_parser(
+        command, formatter_class=argparse.HelpFormatter, parents=parents, add_help=False
+    )
 
     parser.add_argument("application", type=str, help="MONAI application path")
     parser.add_argument(

monai/deploy/runner/run_command.py

@@ -20,7 +20,9 @@
 
 
 def create_run_parser(subparser: _SubParsersAction, command: str, parents: List[ArgumentParser]) -> ArgumentParser:
-    parser = subparser.add_parser(command, formatter_class=HelpFormatter, parents=parents, add_help=False)
+    parser: ArgumentParser = subparser.add_parser(
+        command, formatter_class=HelpFormatter, parents=parents, add_help=False
+    )
 
     parser.add_argument("map", metavar="<map-image[:tag]>", help="MAP image name")
 

run

@@ -301,11 +301,16 @@ get_package_info() {
 #==================================================================================
 
 install_python_dev_deps() {
+    local config="${1:-dev}"
     if [ -n "${VIRTUAL_ENV}" ] || [ -n "${CONDA_PREFIX}" ]; then
-        run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
+        # Read the Docs site is using specific setuptools version so should not upgrade it.
+        if [ "$config" = "read_the_docs" ]; then
+            run_command ${MONAI_PY_EXE} -m pip install -q -U pip wheel build
+        else
+            run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
+        fi
         run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/requirements-dev.txt
         run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/requirements-examples.txt
-
     else
         c_echo_err R "You must be in a virtual environment to install dependencies."
         if [ ! -e "$TOP/.venv/dev/bin/python3" ]; then
@@ -370,10 +375,14 @@ install_edit_mode() {
 }
 
 setup_desc() { c_echo 'Setup development environment
+
+Arguements:
+  $1 - configuration (default: "dev")
 '
 }
 setup() {
-    install_python_dev_deps
+    local config="${1:-dev}"
+    install_python_dev_deps "${config}"
 }
 
 clean_desc() { c_echo 'Clean up temporary files and uninstall monai-deploy-app-sdk
@@ -895,6 +904,7 @@ install_doc_requirements() {
         run_command ${MONAI_PY_EXE} -m pip install -q -U setuptools pip wheel build
         run_command ${MONAI_PY_EXE} -m pip install -q -r ${TOP}/docs/requirements.txt
         install_edit_mode
+        hash -r  # reload hash for sphinx-build command
     else
         c_echo_err R "You must be in a virtual environment to install dependencies."
         if [ ! -e "$TOP/.venv/dev/bin/python3" ]; then
@@ -916,7 +926,7 @@ setup_gen_docs() {
     # Remove existing files in dist/docs
     run_command rm -rf ${output_folder}/*
     # Remove existing _autosummary folder
-    run command rm -rf ${TOP}/docs/source/modules/_autosummary
+    run_command rm -rf ${TOP}/docs/source/modules/_autosummary
 
     # Symbolic link notebooks folder from 'docs/source/notebooks' to 'notebooks'
     run_command rm -rf ${TOP}/docs/source/notebooks