diff --git a/.github/workflows/build_workflow.yml b/.github/workflows/build_workflow.yml index a73ba6b2e..09f123c87 100644 --- a/.github/workflows/build_workflow.yml +++ b/.github/workflows/build_workflow.yml @@ -54,16 +54,15 @@ jobs: - uses: actions/checkout@v3 - name: Set up Conda Environment - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: - activate-environment: "pcmdi_metrics_ci" - miniforge-variant: Mambaforge + miniforge-variant: Miniforge3 miniforge-version: latest + activate-environment: "pcmdi_metrics_ci" environment-file: conda-env/ci.yml - use-mamba: true - mamba-version: "*" channel-priority: strict auto-update-conda: true + python-version: ${{ matrix.python-version }} # Used for refreshing the cache every 24 hours to avoid inconsistencies of package # versions between the CI pipeline and local installations. @@ -79,7 +78,7 @@ jobs: key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ - hashFiles('conda-env/dev.yml') }}-${{ env.CACHE_NUMBER}} + hashFiles('conda-env/ci.yml') }}-${{ env.CACHE_NUMBER}} env: # Increase this value to reset cache if conda/dev.yml has not changed in the workflow CACHE_NUMBER: 0 @@ -118,10 +117,10 @@ jobs: with: path: ~/conda_pkgs_dir key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ - hashFiles('conda-env/ci.yml') }} + hashFiles('conda-env/dev.yml') }} - name: Set up Conda Environment - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: activate-environment: "pcmdi_metrics_dev" miniforge-variant: Miniforge3 diff --git a/doc/jupyter/Demo/Demo_0_download_data.ipynb b/doc/jupyter/Demo/Demo_0_download_data.ipynb index e230e9fec..4b49b5db1 100644 --- a/doc/jupyter/Demo/Demo_0_download_data.ipynb +++ b/doc/jupyter/Demo/Demo_0_download_data.ipynb @@ -8,7 +8,7 @@ "\n", "Download sample data and set up parameter files\n", "\n", - "This Notebook sets up the data for the other demos. It is recommended that you run this and other demos in a conda environment with **xcdat** and **pcmdi_metrics** installed." + "This Notebook sets up the data for the other demos. It is recommended that you run this and other demos in a conda environment with **xcdat** and **pcmdi_metrics** installed. The files to download are listed in https://pcmdiweb.llnl.gov/pss/pmpdata/pmp_tutorial_files.v20240201.txt." ] }, { @@ -52,7 +52,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In below cell, you are going to download sample input files from PCMDI server. The total size of dataset is about 2 GB, and so please be aware that downloading will take some time to complete. List of downloading files can be found in [`data_files.txt`](https://pcmdiweb.llnl.gov/pss/pmpdata/pmp_tutorial_files.v20240201.txt) file." + "In below cell, you are going to download sample input files from PCMDI server. The total size of dataset is about 2 GB, and so please be aware that downloading will take some time to complete." ] }, { diff --git a/doc/jupyter/Demo/Demo_5_mjo_metrics.ipynb b/doc/jupyter/Demo/Demo_5_mjo_metrics.ipynb index fa15c676e..be8a609a6 100644 --- a/doc/jupyter/Demo/Demo_5_mjo_metrics.ipynb +++ b/doc/jupyter/Demo/Demo_5_mjo_metrics.ipynb @@ -391,13 +391,6 @@ "from IPython.display import Image\n", "Image(filename=demo_output_directory+\"/mjo/Ex2/cmip5_GISS-E2-H_historical_r6i1p1_mjo_2000-2005_NDJFMA_cmmGrid.png\")" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/doc/jupyter/Demo/Demo_7_precip_variability.ipynb b/doc/jupyter/Demo/Demo_7_precip_variability.ipynb index 1ca9f8089..24cea7845 100644 --- a/doc/jupyter/Demo/Demo_7_precip_variability.ipynb +++ b/doc/jupyter/Demo/Demo_7_precip_variability.ipynb @@ -889,13 +889,6 @@ " metric = json.load(f)[\"RESULTS\"]\n", "print(json.dumps(metric, indent=2))" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/doc/jupyter/Demo/Demo_8_extremes.ipynb b/doc/jupyter/Demo/Demo_8_extremes.ipynb index bb819012b..bd73fc249 100644 --- a/doc/jupyter/Demo/Demo_8_extremes.ipynb +++ b/doc/jupyter/Demo/Demo_8_extremes.ipynb @@ -2242,14 +2242,6 @@ "%%bash -s \"$demo_output_directory\"\n", "rm -r $1/extremes_tmp" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e8ff050a", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/doc/jupyter/Demo/Demo_9_seaIceExtent_ivanova.ipynb b/doc/jupyter/Demo/Demo_9_seaIceExtent_ivanova.ipynb index dcb6f0b09..6d9c85f45 100644 --- a/doc/jupyter/Demo/Demo_9_seaIceExtent_ivanova.ipynb +++ b/doc/jupyter/Demo/Demo_9_seaIceExtent_ivanova.ipynb @@ -3013,14 +3013,6 @@ "Go back to Top\n", "" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e3b50c5e", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/docs/demo-notebooks.rst b/docs/demo-notebooks.rst index 693d20ff7..fdb69c1fe 100644 --- a/docs/demo-notebooks.rst +++ b/docs/demo-notebooks.rst @@ -54,8 +54,8 @@ Basic Usage Examples examples/parallel_coordinate_plot_example examples/taylor_diagram_example -Real World Use Cases -^^^^^^^^^^^^^^^^^^^^ +Practical Use Cases +^^^^^^^^^^^^^^^^^^^ .. nbgallery:: @@ -65,4 +65,5 @@ Real World Use Cases examples/parallel_coordinate_plot_mean_clim_multiMIPs examples/taylor_diagram_multiple_CMIPs examples/mean_clim_plots_test_model - examples/variability_modes_plots_all-stats \ No newline at end of file + examples/variability_modes_plots_all-stats + examples/return_value_portrait_plot_demo \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 37abf2571..bcc6c91ef 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -81,28 +81,28 @@ BSD 3-Clause License. See `LICENSE .. toctree:: :maxdepth: 1 :hidden: - :caption: For developers/contributors: + :caption: For developers/contributors api contributing resources team - GitHub repository .. toctree:: :maxdepth: 1 :hidden: - :caption: Community + :caption: Links - GitHub discussions + PMP Results + Source Code + Discussions diff --git a/docs/metrics_enso.rst b/docs/metrics_enso.rst index d4da2dd1d..10451281f 100644 --- a/docs/metrics_enso.rst +++ b/docs/metrics_enso.rst @@ -39,4 +39,4 @@ Additional Resources .. _Description for the results: https://pcmdi.llnl.gov/metrics/enso/ .. _Description for included metrics: https://github.com/CLIVAR-PRP/ENSO_metrics/wiki .. _Interactive graphics for PMP-calculated ENSO Metrics: https://pcmdi.llnl.gov/pmp-preliminary-results/interactive_plot/portrait_plot/enso_metric/enso_metrics_interactive_portrait_plots_v20210723.html -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_6_ENSO.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_6_ENSO.html diff --git a/docs/metrics_ext.rst b/docs/metrics_ext.rst index b7a0511a2..57c65113e 100644 --- a/docs/metrics_ext.rst +++ b/docs/metrics_ext.rst @@ -13,11 +13,11 @@ Demo ===== * `PMP demo Jupyter notebook`_ -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_8_extremes.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_8_extremes.html * `Extremes Portrait Plot demo Jupyter notebook`_ -.. _Extremes Portrait Plot demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/pcmdi_metrics/graphics/portrait_plot/return_value_portrait_plot_demo.ipynb +.. _Extremes Portrait Plot demo Jupyter notebook: examples/return_value_portrait_plot_demo Inputs ======== diff --git a/docs/metrics_mean-clim.rst b/docs/metrics_mean-clim.rst index b947d1137..d88770ea7 100644 --- a/docs/metrics_mean-clim.rst +++ b/docs/metrics_mean-clim.rst @@ -20,8 +20,7 @@ Before it can be applied some preparation is needed including: * Construction of an input parameter file to run the desired operations -Each of these steps is included in the -`mean climate notebook `_ +Each of these steps is included in the following demo notebooks along with a series of examples that demonstrate the options. These steps are also summarized below. @@ -110,6 +109,6 @@ In addition to the minimum set of parameters noted above, the following **additi * **save_test_clims** Select to save (or not) interpolated climatologies including masking * **case_id** Save JSON and netCDF files into a subdirectory so that results from multiple tests can be readily organized -.. _PMP demo Jupyter notebook1a: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_1a_compute_climatologies.ipynb -.. _PMP demo Jupyter notebook1b: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_1b_mean_climate.ipynb +.. _PMP demo Jupyter notebook1a: examples/Demo_1a_compute_climatologies.html +.. _PMP demo Jupyter notebook1b: examples/Demo_1b_mean_climate.html diff --git a/docs/metrics_mjo.rst b/docs/metrics_mjo.rst index db5d70ef6..db728af96 100644 --- a/docs/metrics_mjo.rst +++ b/docs/metrics_mjo.rst @@ -56,6 +56,6 @@ References .. _1972: https://doi.org/10.1175/1520-0469(1972)029%3C1109:DOGSCC%3E2.0.CO;2 .. _1994: https://doi.org/10.1175/1520-0493(1994)122%3C0814:OOTDTO%3E2.0.CO;2 -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_5_mjo_metrics.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_5_mjo_metrics.html .. _Interactive graphics for PMP-calculated MJO Metrics: https://pcmdi.llnl.gov/pmp-preliminary-results/interactive_plot/mjo/bar_chart/mjo_ewr_cmip5and6_overlap_runs_average_v20200720.html .. _Description for the results: https://pcmdi.llnl.gov/research/metrics/mjo/ \ No newline at end of file diff --git a/docs/metrics_monsoon.rst b/docs/metrics_monsoon.rst index 380ad9faa..194c29c05 100644 --- a/docs/metrics_monsoon.rst +++ b/docs/metrics_monsoon.rst @@ -21,5 +21,5 @@ References ========== * Sperber, K.R. and Annamalai, H., 2014. The use of fractional accumulated precipitation for the evaluation of the annual cycle of monsoons. Climate Dynamics, 43, 3219-3244, doi:10.1007/s00382-014-2099-3 -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_2b_monsoon_sperber.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_2b_monsoon_sperber.html diff --git a/docs/metrics_mov.rst b/docs/metrics_mov.rst index 5d34d3c22..efc4b4090 100644 --- a/docs/metrics_mov.rst +++ b/docs/metrics_mov.rst @@ -40,6 +40,6 @@ References * Lee, J., K. Sperber, P. Gleckler, K. Taylor, and C. Bonfils, 2021: Benchmarking performance changes in the simulation of extratropical modes of variability across CMIP generations. Journal of Climate, 34, 6945–6969, https://doi.org/10.1175/JCLI-D-20-0832.1 -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_4_modes_of_variability.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_4_modes_of_variability.html .. _Interactive graphics for PMP-calculated MoV Metrics: https://pcmdi.llnl.gov/pmp-preliminary-results/interactive_plot/variability_modes/portrait_plot/pmp_mov_page_viewer.html .. _Description for the results: https://pcmdi.llnl.gov/research/metrics/variability_modes/ \ No newline at end of file diff --git a/docs/metrics_precip-variability.rst b/docs/metrics_precip-variability.rst index 4e7aa14f4..0e1f72c35 100644 --- a/docs/metrics_precip-variability.rst +++ b/docs/metrics_precip-variability.rst @@ -95,6 +95,6 @@ Reference Ahn, M.-S., P. J. Gleckler, J. Lee, A. G. Pendergrass, and C. Jakob, 2022: Benchmarking Simulated Precipitation Variability Amplitude across Timescales. Journal of Climate. https://doi.org/10.1175/JCLI-D-21-0542.1 -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_7_precip_variability.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_7_precip_variability.html .. _this link: https://github.com/PCMDI/pcmdi_metrics/tree/main/pcmdi_metrics/precip_variability/param .. _calc_ratio.py: https://github.com/PCMDI/pcmdi_metrics/blob/main/pcmdi_metrics/precip_variability/scripts_pcmdi/calc_ratio.py diff --git a/docs/metrics_sea_ice.rst b/docs/metrics_sea_ice.rst index 1ccf5e348..0dca12f5f 100644 --- a/docs/metrics_sea_ice.rst +++ b/docs/metrics_sea_ice.rst @@ -13,7 +13,7 @@ Demo ===== * `PMP demo Jupyter notebook`_ -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_9_seaIceExtent_ivanova.ipynb +.. _PMP demo Jupyter notebook: examples/Demo_9_seaIceExtent_ivanova.html Inputs ====== diff --git a/docs/metrics_subdaily-precipitation.rst b/docs/metrics_subdaily-precipitation.rst index f82543f2a..7549b75e9 100644 --- a/docs/metrics_subdaily-precipitation.rst +++ b/docs/metrics_subdaily-precipitation.rst @@ -26,4 +26,4 @@ References -.. _PMP demo Jupyter notebook: https://github.com/PCMDI/pcmdi_metrics/blob/main/doc/jupyter/Demo/Demo_3_diurnal_cycle.ipynb \ No newline at end of file +.. _PMP demo Jupyter notebook: examples/Demo_3_diurnal_cycle.html \ No newline at end of file