Packaging and deployment

.dockerignore

@@ -0,0 +1,82 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+*.egg-info/
+.installed.cfg
+*.egg
+dist/
+build/
+*.whl
+.venv
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# Environments
+.env
+.envrc
+*.env
+
+# VS Code
+.vscode/
+
+# Pycharm
+.idea/
+
+# Docker
+Dockerfile
+docker-compose.yml
+.dockerignore

.gitignore

@@ -84,6 +84,7 @@ celerybeat-schedule
 # virtualenv
 venv/
 ENV/
+.venv/
 
 # Spyder project settings
 .spyderproject

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.11
+
+RUN addgroup --system app && adduser --system --ingroup app app
+WORKDIR /home/app
+RUN chown app:app -R /home/app
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY data data
+COPY gnomad_sumstats_explorer gnomad_sumstats_explorer
+
+EXPOSE 8000
+
+USER app
+ENV PYTHONPATH="."
+CMD [ "shiny", "run", "--host", "0.0.0.0", "--port", "8000", "gnomad_sumstats_explorer/app.py" ]

cloudbuild.yaml

@@ -0,0 +1,12 @@
+steps:
+  - name: 'gcr.io/cloud-builders/docker'
+    args:
+      [
+        'build',
+        '-t',
+        'us-docker.pkg.dev/$PROJECT_ID/gnomad/gnomad-sumstats-explorer:$SHORT_SHA',
+        '.',
+      ]
+
+images:
+  - 'us-docker.pkg.dev/$PROJECT_ID/gnomad/gnomad-sumstats-explorer:$SHORT_SHA'

requirements-dev.in

@@ -1,6 +1,10 @@
 # Used to create the requirements-dev.txt file
 # Note: `pip-compile requirements-dev.in` needs to be run before changes in requirements-dev.in are reflected in
 # requirements-dev.txt, which is used for GitHub Actions
+
+# Constrain to the requirements.txt file to reduce conflicts. When updating, first compile requirements.txt, then
+# requirements-dev.txt
+-c requirements.txt
 black==24.4.2 # This should be kept in sync with the version in .pre-commit-config.yaml
 isort==5.12.0 # This should be kept in sync with the version in .pre-commit-config.yaml
 autopep8==2.0.2 # This should be kept in sync with the version in .pre-commit-config.yaml

requirements-dev.txt

@@ -13,7 +13,9 @@ black==24.4.2
 cfgv==3.4.0
     # via pre-commit
 click==8.1.7
-    # via black
+    # via
+    #   -c requirements.txt
+    #   black
 dill==0.3.8
     # via pylint
 distlib==0.3.8
@@ -32,12 +34,15 @@ mypy-extensions==1.0.0
     # via black
 nodeenv==1.9.1
     # via pre-commit
-packaging==24.1
-    # via black
+packaging==24.2
+    # via
+    #   -c requirements.txt
+    #   black
 pathspec==0.12.1
     # via black
-platformdirs==4.2.2
+platformdirs==4.3.6
     # via
+    #   -c requirements.txt
     #   black
     #   pylint
     #   virtualenv

requirements.in

@@ -0,0 +1,6 @@
+faicons
+shiny
+shinywidgets
+seaborn
+pandas
+plotly

requirements.txt

@@ -1,6 +1,167 @@
-faicons
-shiny
-shinywidgets
-seaborn
-pandas
-plotly
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+anyio==4.6.2.post1
+    # via
+    #   starlette
+    #   watchfiles
+appdirs==1.4.4
+    # via shiny
+asgiref==3.8.1
+    # via shiny
+asttokens==2.4.1
+    # via stack-data
+click==8.1.7
+    # via
+    #   shiny
+    #   uvicorn
+comm==0.2.2
+    # via ipywidgets
+contourpy==1.3.0
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+decorator==5.1.1
+    # via ipython
+executing==2.1.0
+    # via stack-data
+faicons==0.2.2
+    # via -r requirements.in
+fonttools==4.54.1
+    # via matplotlib
+h11==0.14.0
+    # via uvicorn
+htmltools==0.6.0
+    # via
+    #   faicons
+    #   shiny
+idna==3.10
+    # via anyio
+ipython==8.18.0
+    # via ipywidgets
+ipywidgets==8.1.5
+    # via shinywidgets
+jedi==0.19.1
+    # via ipython
+jupyter-core==5.7.2
+    # via shinywidgets
+jupyterlab-widgets==3.0.13
+    # via ipywidgets
+kiwisolver==1.4.7
+    # via matplotlib
+linkify-it-py==2.0.3
+    # via shiny
+markdown-it-py==3.0.0
+    # via
+    #   mdit-py-plugins
+    #   shiny
+matplotlib==3.9.2
+    # via seaborn
+matplotlib-inline==0.1.7
+    # via ipython
+mdit-py-plugins==0.4.2
+    # via shiny
+mdurl==0.1.2
+    # via markdown-it-py
+narwhals==1.13.3
+    # via shiny
+numpy==2.1.3
+    # via
+    #   contourpy
+    #   matplotlib
+    #   pandas
+    #   seaborn
+orjson==3.10.11
+    # via shiny
+packaging==24.2
+    # via
+    #   htmltools
+    #   matplotlib
+    #   plotly
+    #   shiny
+pandas==2.2.3
+    # via
+    #   -r requirements.in
+    #   seaborn
+parso==0.8.4
+    # via jedi
+pexpect==4.9.0
+    # via ipython
+pillow==11.0.0
+    # via matplotlib
+platformdirs==4.3.6
+    # via jupyter-core
+plotly==5.24.1
+    # via -r requirements.in
+prompt-toolkit==3.0.36
+    # via
+    #   ipython
+    #   questionary
+    #   shiny
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pygments==2.18.0
+    # via ipython
+pyparsing==3.2.0
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   pandas
+    #   shinywidgets
+python-multipart==0.0.17
+    # via shiny
+pytz==2024.2
+    # via pandas
+questionary==2.0.1
+    # via shiny
+seaborn==0.13.2
+    # via -r requirements.in
+shiny==1.2.0
+    # via
+    #   -r requirements.in
+    #   shinywidgets
+shinywidgets==0.3.4
+    # via -r requirements.in
+six==1.16.0
+    # via
+    #   asttokens
+    #   python-dateutil
+sniffio==1.3.1
+    # via anyio
+stack-data==0.6.3
+    # via ipython
+starlette==0.41.2
+    # via shiny
+tenacity==9.0.0
+    # via plotly
+traitlets==5.14.3
+    # via
+    #   comm
+    #   ipython
+    #   ipywidgets
+    #   jupyter-core
+    #   matplotlib-inline
+typing-extensions==4.12.2
+    # via
+    #   htmltools
+    #   shiny
+tzdata==2024.2
+    # via pandas
+uc-micro-py==1.0.3
+    # via linkify-it-py
+uvicorn==0.32.0
+    # via shiny
+watchfiles==0.24.0
+    # via shiny
+wcwidth==0.2.13
+    # via prompt-toolkit
+websockets==13.1
+    # via shiny
+widgetsnbextension==4.0.13
+    # via ipywidgets