Add dockerfile for running PTM in a container (#38)

* Add if-main clause to cli

* Move top-level confest.py to project root

* Add dockerfile

* Remove extra whitespace

* Upgrade micromamba base image

* Undo style change

* Add __init__ file to tests root directory

* updates to get tests working locally

One still does not work but it will with a change in my next PR

* Fix precommit error

---------

Co-authored-by: Kristen Thyng <kthyng@gmail.com>

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ repos:
   rev: 1.6.0
   hooks:
     - id: interrogate
-      exclude: ^(docs|setup.py|tests)
+      exclude: ^(docs|setup.py|tests|conftest.py)
       args: [--config=pyproject.toml]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks

Dockerfile

@@ -0,0 +1,17 @@
+FROM mambaorg/micromamba:2.0.5-debian12
+
+ENV PROJECT_NAME=particle-tracking-manager
+ENV PROJECT_ROOT=/opt/particle-tracking-manager
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+RUN micromamba install -y -n base -f /tmp/environment.yml && \
+    micromamba clean --all --yes && \
+    rm /tmp/environment.yml
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER particle_tracking_manager $PROJECT_ROOT/particle_tracking_manager
+COPY --chown=$MAMBA_USER:$MAMBA_USER tests $PROJECT_ROOT/tests
+COPY --chown=$MAMBA_USER:$MAMBA_USER pyproject.toml setup.cfg conftest.py README.md $PROJECT_ROOT/
+
+WORKDIR $PROJECT_ROOT/
+
+ENTRYPOINT ["micromamba", "run", "python", "-m", "particle_tracking_manager.cli"]

particle_tracking_manager/cli.py

@@ -179,3 +179,7 @@ def main():
     # # Remove the handler at the end of the loop
     # m.logger.removeHandler(file_handler)
     # file_handler.close()
+
+
+if __name__ == "__main__":
+    main()

tests/test_cli.py

@@ -15,7 +15,7 @@ def test_setup():
     No drifters are run due to oceanmodel=None
     """
     ret_value = os.system(
-        f"python {ptm.__path__[0]}/cli.py ocean_model=test lon=-151 lat=59 use_auto_landmask=True start_time='2000-1-1'"
+        f"ptm ocean_model=test lon=-151 lat=59 use_auto_landmask=True start_time='2000-1-1' --dry-run"
     )
     assert ret_value == 0