Feat/add syracuse qdr retriever (#1)

* (HP-1459): update README and gitignore

* (HP-1459): add pyproject.toml, poetry.lock

* (HP-1459): add qdr_downloads module

* (HP-1459): add unit tests

* (HP-1459): add ci.yaml and ci_commands_script.sh

* (HP-1459): add image_build_push and wool

* (HP-1459): add secrets.baseline and pre-commit-config

* (HP-1459): expand documentation for qdr_download

* (HP-1459): use streaming in download

* (HP-1459): clean up tests

* (HP-1459): clean up request_headers test

* (HP-1459): clean up tests

* (HP-1459): clean up comments

* (HP-1459): add content to README

* (HP-1459): remove github action for 'image_build_push'

* (HP-1459): handle None download_url

* (HP-1459): allow downloading of single files, unzipped

* (HP-1459): get file_ids one at a time

* (HP-1459): remove unused variable

* (HP-1459): remove debug statements

* (HP-1459): add instructions for pip install from repo

* (HP-1459): move 'pip install' section further down in README

---------

Co-authored-by: Mingfei Shao <[email protected]>

.gitignore

@@ -1,3 +1,6 @@
+*.DS_Store
+*.vscode
+.idea
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -27,8 +30,6 @@ share/python-wheels/
 MANIFEST
 
 # 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
 
@@ -83,31 +84,7 @@ profile_default/
 ipython_config.py
 
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
+.python-version
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
@@ -152,9 +129,4 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# pytest output

README.md

@@ -1 +1,40 @@
-# heal-platform-sdk
+# heal-platform-sdk
+
+The HEAL Platform Software Development Kit (SDK) for Python provides classes and functions for handling HEAL specific tasks.
+
+### qdr_downloads
+
+The qdr_downloads module include a retriever function for downloading files from Syracuse QDR.
+
+This is intended to be called by gen3sdk [external download functions](https://github.com/uc-cdis/gen3sdk-python/blob/master/gen3/tools/download/external_file_download.py). It is also possible to write a wrapper script for the qdr download functions.
+
+### Run tests
+
+```
+poetry run pytest -vv tests
+```
+
+### Pip install for using heal-platform-sdk
+
+Until the `heal-platform-sdk` is available on PyPI, any local pip installs should directly
+reference the git repo.
+
+As an example, `pip install` can be called from the command line for getting
+the master branch of the `heal-platform-sdk`,
+
+```
+pip install -e git+ssh://[email protected]/uc-cdis/heal-platform-sdk.git#egg=heal
+```
+
+or a particular branch, eg,
+
+```
+pip install -e git+ssh://[email protected]/uc-cdis/heal-platform-sdk.git@feat/add-syracuse-qdr-retriever#egg=heal
+```
+
+The specification can also be listed in requirements.txt file
+(with, say, a tag specification of 0.1.0)
+
+```
+-e git+ssh://[email protected]/uc-cdis/[email protected]#egg=heal
+```

heal/__init__.py

@@ -0,0 +1,4 @@
+from cdislogging import get_logger
+
+LOG_FORMAT = "[%(asctime)s][%(levelname)7s] %(message)s"
+logging = get_logger("__name__", format=LOG_FORMAT, log_level="info")