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Standardize Python exec commands to python -m (#340)
Replaced `python3 -m` usage with `python -m` across the codebase and documentation for consistency. This ensures alignment with modern Python practices.
1 parent 5f6b58f commit 6db322f

19 files changed

+77
-77
lines changed

‎.github/workflows/pytest-with-coverage.yaml

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@@ -37,16 +37,16 @@ jobs:
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- name: Install editable-mode dependency packages
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shell: bash -l {0}
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run: |
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/43ravens/NEMO_Nowcast.git#egg=NEMO_Nowcast
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/moad_tools#egg=moad_tools
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/Reshapr#egg=Reshapr
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/NEMO-Cmd.git#egg=NEMO-Cmd
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/SalishSeaCmd.git#egg=SalishSeaCmd
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable "git+https://github.com/SalishSeaCast/tools#egg=SalishSeaTools&subdirectory=SalishSeaTools"
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/FVCOM-Cmd.git#egg=FVCOM-Cmd
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/43ravens/NEMO_Nowcast.git#egg=NEMO_Nowcast
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/moad_tools#egg=moad_tools
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/Reshapr#egg=Reshapr
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/NEMO-Cmd.git#egg=NEMO-Cmd
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/SalishSeaCmd.git#egg=SalishSeaCmd
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable "git+https://github.com/SalishSeaCast/tools#egg=SalishSeaTools&subdirectory=SalishSeaTools"
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/FVCOM-Cmd.git#egg=FVCOM-Cmd
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# OPPTools is a private GitLab repo, so an access token is required
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python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://oauth2:${{ secrets.GITLAB_ACCESS_TOKEN }}@gitlab.com/mdunphy/OPPTools.git@6c784a4dc44dd9030aafe9a8519e5ae0b6cc3183#egg=OPPTools
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python3 -m pip install --editable $GITHUB_WORKSPACE
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python -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://oauth2:${{ secrets.GITLAB_ACCESS_TOKEN }}@gitlab.com/mdunphy/OPPTools.git@6c784a4dc44dd9030aafe9a8519e5ae0b6cc3183#egg=OPPTools
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python -m pip install --editable $GITHUB_WORKSPACE
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- name: pytest package with coverage
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shell: bash -l {0}

‎config/nowcast.yaml

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@@ -4,7 +4,7 @@
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checklist file: $(NOWCAST.ENV.NOWCAST_LOGS)/nowcast_checklist.yaml
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# Python interpreter in environment with all dependencies installed
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python: $(NOWCAST.ENV.NOWCAST_ENV)/bin/python3
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python: $(NOWCAST.ENV.NOWCAST_ENV)/bin/python
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# Filesystem group name to use for ownership of newly created files
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file group: sallen
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# Python interpreter on compute host in an environment with all
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# dependencies installed. Used to, for example, launch run_NEMO and
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# watch_NEMO workers.
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python: /nemoShare/MEOPAR/nowcast-sys/nowcast-env/bin/python3
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python: /nemoShare/MEOPAR/nowcast-sys/nowcast-env/bin/python
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# Location on the compute host of the nowcast system config file
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config file: /nemoShare/MEOPAR/nowcast-sys/SalishSeaNowcast/config/nowcast.yaml
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# Directory on compute host where files (e.g. namelist.time) and symlinks

‎docs/deployment/optimum.rst

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@@ -217,15 +217,15 @@ Load the ``Miniconda/3`` module and create a Conda environment:
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$ conda create -n salishseacast -c conda-forge python=3 pip arrow \
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attrs cliff f90nml gitpython pyyaml
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$ source activate salishseacast
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(salishseacast)$ python3 -m pip install python-hglib
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(salishseacast)$ python -m pip install python-hglib
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Install the SalishSeaCast NEMO-Cmd and SalishSeaCmd packages from their repo clones:
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.. code-block:: bash
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(salishseacast)$ cd $PROJECT/SalishSeaCast/hindcast-sys/
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(salishseacast)$ python3 -m pip install --editable NEMO-Cmd/
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(salishseacast)$ python3 -m pip install --editable SalishSeaCmd/
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(salishseacast)$ python -m pip install --editable NEMO-Cmd/
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(salishseacast)$ python -m pip install --editable SalishSeaCmd/
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Populate Run Preparation Directory

‎docs/deployment/skookum.rst

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@@ -109,7 +109,7 @@ For the `salishsea-site web app`_ that is mounted at https://salishsea.eos.ubc.c
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--prefix /SalishSeaCast/salishsea-site-env \
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-f salishsea-site/envs/environment-prod.yaml
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$ mamba activate /SalishSeaCast/salishsea-site-env
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(/SalishSeaCast/salishsea-site-env) $ python3 -m pip install --editable salishsea-site/
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(/SalishSeaCast/salishsea-site-env) $ python -m pip install --editable salishsea-site/
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Environment Variables

‎docs/figures/fig_dev_env.rst

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@@ -70,14 +70,14 @@ you can create and activate a figures development environment with these command
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$ cd SalishSeaNowcast
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$ conda env create -f envs/environment-fig-dev.yaml
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$ conda activate nowcast-fig-dev
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(nowcast-fig-dev)$ python3 -m pip install --editable ../NEMO_Nowcast
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(nowcast-fig-dev)$ python3 -m pip install --editable ../moad_tools
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(nowcast-fig-dev)$ python3 -m pip install --editable ../Reshapr
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(nowcast-fig-dev)$ python3 -m pip install --editable ../tools/SalishSeaTools
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(nowcast-fig-dev)$ python3 -m pip install --editable ../NEMO-Cmd
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(nowcast-fig-dev)$ python3 -m pip install --editable ../SalishSeaCmd
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(nowcast-fig-dev)$ python3 -m pip install --editable ../salishsea-site/
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(nowcast-fig-dev)$ python3 -m pip install --editable .
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(nowcast-fig-dev)$ python -m pip install --editable ../NEMO_Nowcast
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(nowcast-fig-dev)$ python -m pip install --editable ../moad_tools
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(nowcast-fig-dev)$ python -m pip install --editable ../Reshapr
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(nowcast-fig-dev)$ python -m pip install --editable ../tools/SalishSeaTools
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(nowcast-fig-dev)$ python -m pip install --editable ../NEMO-Cmd
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(nowcast-fig-dev)$ python -m pip install --editable ../SalishSeaCmd
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(nowcast-fig-dev)$ python -m pip install --editable ../salishsea-site/
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(nowcast-fig-dev)$ python -m pip install --editable .
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The ``--editable`` option in the :command:`pip install` command above installs the packages from the cloned repos via symlinks so that the installed packages will be automatically updated as the repos evolve.
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‎docs/pkg_development.rst

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@@ -163,18 +163,18 @@ the commands below install the packages into your ``salishsea-nowcast`` developm
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$ cd SalishSeaNowcast
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$ conda env create -f envs/environment-dev.yaml
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$ conda activate salishsea-nowcast
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(salishsea-nowcast)$ python3 -m pip install --editable ../NEMO_Nowcast
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(salishsea-nowcast)$ python3 -m pip install --editable ../moad_tools
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(salishsea-nowcast)$ python3 -m pip install --editable ../Reshapr
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(salishsea-nowcast)$ python3 -m pip install --editable ../tools/SalishSeaTools
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(salishsea-nowcast)$ python -m pip install --editable ../NEMO_Nowcast
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(salishsea-nowcast)$ python -m pip install --editable ../moad_tools
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(salishsea-nowcast)$ python -m pip install --editable ../Reshapr
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(salishsea-nowcast)$ python -m pip install --editable ../tools/SalishSeaTools
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(salishsea-nowcast)$ cd ../OPPTools
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(salishsea-nowcast)$ git switch SalishSeaCast-prod
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(salishsea-nowcast)$ cd ../SalishSeaNowcast
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(salishsea-nowcast)$ python3 -m pip install --editable OPPTools
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(salishsea-nowcast)$ python3 -m pip install --editable ../NEMO-Cmd
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(salishsea-nowcast)$ python3 -m pip install --editable ../SalishSeaCmd
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(salishsea-nowcast)$ python3 -m pip install --editable ../FVCOM-Cmd
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(salishsea-nowcast)$ python3 -m pip install --editable .
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(salishsea-nowcast)$ python -m pip install --editable OPPTools
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(salishsea-nowcast)$ python -m pip install --editable ../NEMO-Cmd
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(salishsea-nowcast)$ python -m pip install --editable ../SalishSeaCmd
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(salishsea-nowcast)$ python -m pip install --editable ../FVCOM-Cmd
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(salishsea-nowcast)$ python -m pip install --editable .
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The ``--editable`` option in the :command:`pip install` command above installs the packages from the cloned repos via symlinks so that the installed packages will be automatically updated as the repos evolve.
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‎docs/worker_failures.rst

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@@ -87,7 +87,7 @@ then run the worker as follows:
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.. code-block:: bash
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(/SalishSeaCast/nowcast-env)skookum$ python3 -m nowcast.workers.download_weather $NOWCAST_YAML 12 2.5km --debug
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(/SalishSeaCast/nowcast-env)skookum$ python -m nowcast.workers.download_weather $NOWCAST_YAML 12 2.5km --debug
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The command above downloads the 12 forecast.
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The ``--debug`` flag causes the logging output of the worker to be displayed

‎envs/environment-dev.yaml

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@@ -6,15 +6,15 @@
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#
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# $ conda env create -f SalishSeaNowcast/envs/environment-dev.yaml
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# $ conda activate salishsea-nowcast
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# $ python3 -m pip install --editable NEMO_Nowcast/
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# $ python3 -m pip install --editable moad_tools/
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# $ python3 -m pip install --editable tools/SalishSeaTools/
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# $ python3 -m pip install --editable Reshapr/
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# $ python3 -m pip install --editable OPPTools/
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# $ python3 -m pip install --editable NEMO-Cmd/
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# $ python3 -m pip install --editable SalishSeaCmd/
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# $ python3 -m pip install --editable FVCOM-Cmd/
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# $ python3 -m pip install --editable SalishSeaNowcast/
9+
# $ python -m pip install --editable NEMO_Nowcast/
10+
# $ python -m pip install --editable moad_tools/
11+
# $ python -m pip install --editable tools/SalishSeaTools/
12+
# $ python -m pip install --editable Reshapr/
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# $ python -m pip install --editable OPPTools/
14+
# $ python -m pip install --editable NEMO-Cmd/
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# $ python -m pip install --editable SalishSeaCmd/
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# $ python -m pip install --editable FVCOM-Cmd/
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# $ python -m pip install --editable SalishSeaNowcast/
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name: salishsea-nowcast
2020

‎envs/environment-fig-dev.yaml

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#
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# $ conda env create -f SalishSeaNowcast/envs/environment-fig-dev.yaml
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# $ conda activate nowcast-fig-dev
8-
# $ python3 -m pip install --editable NEMO_Nowcast/
9-
# $ python3 -m pip install --editable moad_tools/
10-
# $ python3 -m pip install --editable Reshapr/
11-
# $ python3 -m pip install --editable tools/SalishSeaTools/
12-
# $ python3 -m pip install --editable NEMO-Cmd/
13-
# $ python3 -m pip install --editable SalishSeaCmd/
14-
# $ python3 -m pip install --editable SalishSeaNowcast/
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# $ python3 -m pip install --editable salishsea-site/
8+
# $ python -m pip install --editable NEMO_Nowcast/
9+
# $ python -m pip install --editable moad_tools/
10+
# $ python -m pip install --editable Reshapr/
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# $ python -m pip install --editable tools/SalishSeaTools/
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# $ python -m pip install --editable NEMO-Cmd/
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# $ python -m pip install --editable SalishSeaCmd/
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# $ python -m pip install --editable SalishSeaNowcast/
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# $ python -m pip install --editable salishsea-site/
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name: nowcast-fig-dev
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‎envs/environment-prod.yaml

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#
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# $ conda env create -f SalishSeaNowcast/envs/environment-prod.yaml
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# $ conda activate nowcast-env
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# $ python3 -m pip install --editable NEMO_Nowcast/
10-
# $ python3 -m pip install --editable moad_tools/
11-
# $ python3 -m pip install --editable tools/SalishSeaTools/
12-
# $ python3 -m pip install --editable Reshapr/
13-
# $ python3 -m pip install --editable OPPTools/
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# $ python3 -m pip install --editable NEMO-Cmd/
15-
# $ python3 -m pip install --editable SalishSeaCmd/
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# $ python3 -m pip install --editable FVCOM-Cmd/
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# $ python3 -m pip install --editable SalishSeaNowcast/
9+
# $ python -m pip install --editable NEMO_Nowcast/
10+
# $ python -m pip install --editable moad_tools/
11+
# $ python -m pip install --editable tools/SalishSeaTools/
12+
# $ python -m pip install --editable Reshapr/
13+
# $ python -m pip install --editable OPPTools/
14+
# $ python -m pip install --editable NEMO-Cmd/
15+
# $ python -m pip install --editable SalishSeaCmd/
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# $ python -m pip install --editable FVCOM-Cmd/
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# $ python -m pip install --editable SalishSeaNowcast/
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name: nowcast-env
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‎envs/requirements-sarracenia.txt

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# to create an isolated production environment.
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#
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# Create/update this file with:
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# (sarracenia-env)$ python3 -m pip list --format=freeze >> envs/requirements-sarracenia.txt
8+
# (sarracenia-env)$ python -m pip list --format=freeze >> envs/requirements-sarracenia.txt
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amqp==5.1.0
1111
appdirs==1.4.4

‎notebooks/figures/fvcom/research/make_readme.py

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or change the description of a notebook in its first Markdown cell,
2020
please generate a updated `README.md` file with:
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python3 -m make_readme
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python -m make_readme
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and commit and push the updated `README.md` to GitHub.
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"""

‎notebooks/make_readme.py

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or change the description of a notebook in its first Markdown cell,
2020
please generate a updated `README.md` file with:
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22-
python3 -m make_readme
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python -m make_readme
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and commit and push the updated `README.md` to GitHub.
2525
"""

‎nowcast/daily_river_flows.py

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@@ -530,7 +530,7 @@ def _calc_runoff_dataset(obs_date, runoff_array, config):
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"rivers_watersheds_proportions": "salishsea_tools.river_202108",
531531
"history": (
532532
f"[{arrow.now('local').format('ddd YYYY-MM-DD HH:mm:ss ZZ')}] "
533-
f"python3 -m nowcast.workers.make_runoff_file $NOWCAST_YAML "
533+
f"python -m nowcast.workers.make_runoff_file $NOWCAST_YAML "
534534
f"--run-date {obs_date.format('YYYY-MM-DD')}"
535535
),
536536
},

‎nowcast/workers/make_v202111_runoff_file.py

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@@ -613,7 +613,7 @@ def _calc_runoff_dataset(obs_date, runoff_array, config):
613613
],
614614
"history": (
615615
f"[{arrow.now('local').format('ddd YYYY-MM-DD HH:mm:ss ZZ')}] "
616-
f"python3 -m nowcast.workers.make_v202111_runoff_file $NOWCAST_YAML "
616+
f"python -m nowcast.workers.make_v202111_runoff_file $NOWCAST_YAML "
617617
f"--run-date {obs_date_yyyymmdd}"
618618
),
619619
},

‎pyproject.toml

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@@ -92,16 +92,16 @@ dependencies = [
9292
"utm",
9393
"watchdog",
9494
"xarray == 2025.1.1",
95-
# 'NEMO_Nowcast', # use python3 -m pip install --editable NEMO_Nowcast/
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# 'moad_tools', # use python3 -m pip install --editable moad_tools
97-
# 'Reshapr', # use python3 -m pip install --editable Reshapr
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# 'SalishSeaTools', # use python3 -m pip install --editable tools/SalishSeaTools/
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# 'Reshapr', # use python3 -m pip install --editable Reshapr/
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# 'OPPTools', # use python3 -m pip install --editable OPPTools/
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# 'NEMO-Cmd', # use python3 -m pip install --editable NEMO-Cmd/
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# 'SalishSeaCmd', # use python3 -m pip install --editable SalishSeaCmd/
103-
# 'FVCOM-Cmd', # use python3 -m pip install --editable FVCOM-Cmd/
104-
# 'SalishSeaNowcast', # use python3 -m pip install -e SalishSeaNowcast/
95+
# 'NEMO_Nowcast', # use python -m pip install --editable NEMO_Nowcast/
96+
# 'moad_tools', # use python -m pip install --editable moad_tools
97+
# 'Reshapr', # use python -m pip install --editable Reshapr
98+
# 'SalishSeaTools', # use python -m pip install --editable tools/SalishSeaTools/
99+
# 'Reshapr', # use python -m pip install --editable Reshapr/
100+
# 'OPPTools', # use python -m pip install --editable OPPTools/
101+
# 'NEMO-Cmd', # use python -m pip install --editable NEMO-Cmd/
102+
# 'SalishSeaCmd', # use python -m pip install --editable SalishSeaCmd/
103+
# 'FVCOM-Cmd', # use python -m pip install --editable FVCOM-Cmd/
104+
# 'SalishSeaNowcast', # use python -m pip install -e SalishSeaNowcast/
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]
106106

107107
[project.urls]

‎tests/test_config.py

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@@ -34,7 +34,7 @@ def test_checklist_file(self, prod_config, tmpdir):
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3535
def test_python(self, prod_config, tmpdir):
3636
# Config.load() transforms NOWCAST.ENV part of envvars
37-
assert prod_config["python"] == f"{tmpdir}/nowcast-env/bin/python3"
37+
assert prod_config["python"] == f"{tmpdir}/nowcast-env/bin/python"
3838

3939

4040
class TestLoggingPublisher:

‎tests/test_daily_river_flows.py

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@@ -1496,7 +1496,7 @@ def mock_now(tz):
14961496
)
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assert runoff_ds.attrs["history"] == (
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f"[Thu {obs_date.format('YYYY-MM-DD')} 14:51:43 -07:00] "
1499-
f"python3 -m nowcast.workers.make_runoff_file $NOWCAST_YAML "
1499+
f"python -m nowcast.workers.make_runoff_file $NOWCAST_YAML "
15001500
f"--run-date {obs_date.format('YYYY-MM-DD')}"
15011501
)
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‎tests/workers/test_make_v202111_runoff_file.py

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19201920
)
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assert runoff_ds.attrs["history"] == (
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f"[Thu {obs_date.format('YYYY-MM-DD')} 14:51:43 -07:00] "
1923-
f"python3 -m nowcast.workers.make_v202111_runoff_file $NOWCAST_YAML "
1923+
f"python -m nowcast.workers.make_v202111_runoff_file $NOWCAST_YAML "
19241924
f"--run-date {obs_date.format('YYYY-MM-DD')}"
19251925
)
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