Check/Update/Pin dependencies (#104)

* MNT: pin pyart to 1.12.7 * MNT: pin jupyter-book to 0.12.3 * MNT: fix wradlib links * MNT: pin all necessary dependencies in environment.yaml * MNT: force repo2docker version 2022.02.0
openradar · Feb 21, 2024 · 97edb29 · 97edb29
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diff --git a/.github/workflows/build-book-pullrequest.yaml b/.github/workflows/build-book-pullrequest.yaml
@@ -46,6 +46,8 @@ jobs:
           PUBLIC_REGISTRY_CHECK: true
           APPENDIX_FILE: "binder/appendix.txt"
           REPO2DOCKER_EXTRA_ARGS: --Repo2Docker.base_image=docker.io/library/buildpack-deps:bionic
+          FORCE_REPO2DOCKER_VERSION: jupyter-repo2docker==2022.02.0
+
       - name: list docker images
         run: |
           docker image ls -a

diff --git a/.github/workflows/build-book.yaml b/.github/workflows/build-book.yaml
@@ -42,6 +42,7 @@ jobs:
           PUBLIC_REGISTRY_CHECK: true
           APPENDIX_FILE: "binder/appendix.txt"
           REPO2DOCKER_EXTRA_ARGS: --Repo2Docker.base_image=docker.io/library/buildpack-deps:bionic
+          FORCE_REPO2DOCKER_VERSION: jupyter-repo2docker==2022.02.0
 
   build-book:
     runs-on: ubuntu-latest

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -3,22 +3,23 @@ channels:
   - conda-forge
 dependencies:
   - python=3.9
-  - jupyter-book
-  - numpy
-  - scipy
-  - matplotlib
-  - cartopy
-  - pandas
-  - xarray
+  - jupyter-book=0.12.3
+  - numpy<=1.23.2
+  - scipy<=1.9.1
+  - matplotlib<=3.5.3
+  - cartopy<=0.20.3
+  - pandas<=1.4.3
+  - xarray<=2022.6.0
   - wradlib=1.16.2
-  - dask
-  - tqdm
-  - hvplot
-  - rioxarray
-  - geopandas
-  - datashader
-  - pyrad_arm
-  - cookiecutter
+  - dask<=2022.8.1
+  - tqdm<=4.64.0
+  - hvplot<=0.8.0
+  - rioxarray<=0.12.0
+  - geopandas<=0.11.1
+  - datashader<=0.14.2
+  - arm_pyart=1.12.7
+  - pyrad_arm<=0.6.0
+  - cookiecutter<=2.1.1
   # this is needed for baltrad compilation
   - compilers
   - make
@@ -32,10 +33,9 @@ dependencies:
   - libblas=*=*netlib
   - liblapacke=*=*netlib
   # this is needed for notebooks
-  - pip
-  - pyviz_comms>=2.0
-  - nbstripout
+  - pip<=22.2.2
+  - pyviz_comms>=2.0,<3
+  - nbstripout<=0.6.0
   - zip
   - pip:
-      - git+https://github.com/ARM-DOE/pyart.git
       - sphinx-pythia-theme
diff --git a/environment.yml b/environment.yml
@@ -3,24 +3,24 @@ channels:
   - conda-forge
 dependencies:
   - python=3.9
-  - jupyter-book
-  - pip
+  - jupyter-book=0.12.3
+  - pip<=22.2.2
   - wradlib=1.16.2
-  - dask
-  - tqdm
-  - hvplot
-  - rioxarray
-  - geopandas
-  - datashader
-  - arm_pyart
-  - pyrad_arm
-  - cartopy
-  - matplotlib
-  - numpy
-  - xarray
-  - metpy
-  - nbstripout
-  - cookiecutter
+  - dask<=2022.8.1
+  - tqdm<=4.64.0
+  - hvplot<=0.8.0
+  - rioxarray<=0.12.0
+  - geopandas<=0.11.1
+  - datashader<=0.14.2
+  - arm_pyart=1.12.7
+  - pyrad_arm<=0.6.0
+  - matplotlib<=3.5.3
+  - cartopy<=0.20.3
+  - numpy<=1.23.2
+  - xarray<=2022.6.0
+  - metpy<=1.3.1
+  - nbstripout<=0.6.0
+  - cookiecutter<=2.1.1
   # this is needed for baltrad compilation
   - compilers
   - make

diff --git a/notebooks/wradlib/wradlib_data_quality.ipynb b/notebooks/wradlib/wradlib_data_quality.ipynb
@@ -67,11 +67,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import glob\n",
@@ -100,11 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "fglob = \"../pyart/data/example_pyrad/22179/MLL22179/MLL2217907250U*.nc\"\n",
@@ -116,11 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "ds = [xr.open_dataset(f, group=\"sweep_1\", engine=\"cfradial1\", chunks={}) for f in flist]"
@@ -129,11 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "vol = wrl.io.RadarVolume(engine=\"cfradial1\")\n",
@@ -144,11 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "display(vol)"
@@ -166,11 +146,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "sweep_number = 3\n",
@@ -193,11 +169,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "def extract_clutter(da, wsize=5, thrsnorain=0, tr1=6.0, n_p=6, tr2=1.3, rm_nans=False):\n",
@@ -230,11 +202,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "swp = vol[sweep_number]\n",
@@ -267,11 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "fig = plt.figure(figsize=(15, 12))\n",
@@ -320,11 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "extent = wrl.zonalstats.get_bbox(swpx.x.values, swpx.y.values)\n",
@@ -334,11 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# apply fake token, data is already available\n",
@@ -352,11 +308,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "elevation = wrl.georef.read_gdal_values(dem)\n",
@@ -366,11 +318,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "elev = xr.DataArray(\n",
@@ -391,11 +339,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "fig = plt.figure(figsize=(13, 10))\n",
@@ -423,11 +367,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import hvplot\n",
@@ -446,11 +386,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "cl = (\n",
@@ -495,11 +431,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "rastervalues, rastercoords, proj = wrl.georef.extract_raster_dataset(\n",
@@ -529,11 +461,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "PBB = wrl.qual.beam_block_frac(polarvalues, swpx.z.values, beamradius)\n",
@@ -544,11 +472,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "CBB = wrl.qual.cum_beam_block_frac(PBB)\n",
@@ -565,11 +489,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "jupyter": {
-     "outputs_hidden": false
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# just a little helper function to style x and y axes of our maps\n",
@@ -836,7 +756,7 @@
     "- [dask](https://docs.dask.org/)\n",
     "- [gdal](https://gdal.org/index.html)\n",
     "- [hvplot](https://hvplot.holoviz.org/)\n",
-    "- [wradlib xarray backends](https://docs.wradlib.org/en/stable/notebooks/fileio/wradlib_xarray_backends.html)\n",
+    "- [wradlib xarray backends](https://docs.wradlib.org/projects/old-docs/en/1.16.0/notebooks/fileio/wradlib_xarray_backends.html)\n",
     "- [CfRadial1](https://ncar.github.io/CfRadial/)\n",
     "- [OPERA ODIM_H5](https://www.eumetnet.eu/activities/observations-programme/current-activities/opera/)\n",
     "- [WMO JET-OWR](https://community.wmo.int/governance/commission-membership/commission-observation-infrastructure-and-information-systems-infcom/commission-infrastructure-officers/infcom-management-group/standing-committee-measurements-instrumentation-and-traceability-sc-mint/joint-expert-team)"

diff --git a/notebooks/wradlib/wradlib_differential_phase.ipynb b/notebooks/wradlib/wradlib_differential_phase.ipynb
@@ -18,7 +18,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "---"
+    "***"
    ]
   },
   {
@@ -1036,7 +1036,7 @@
     "\n",
     "- [xarray](https://docs.xarray.dev)\n",
     "- [dask](https://docs.dask.org/)\n",
-    "- [wradlib xarray backends](https://docs.wradlib.org/en/stable/notebooks/fileio/wradlib_xarray_backends.html)\n",
+    "- [wradlib xarray backends](https://docs.wradlib.org/projects/old-docs/en/1.16.0/notebooks/fileio/wradlib_xarray_backends.html)\n",
     "- [OPERA ODIM_H5](https://www.eumetnet.eu/activities/observations-programme/current-activities/opera/)\n",
     "- [WMO JET-OWR](https://community.wmo.int/governance/commission-membership/commission-observation-infrastructure-and-information-systems-infcom/commission-infrastructure-officers/infcom-management-group/standing-committee-measurements-instrumentation-and-traceability-sc-mint/joint-expert-team)\n",
     "- Testud, J., Le Bouar, E., Obligis, E., & Ali-Mehenni, M. (2000). The Rain Profiling Algorithm Applied to Polarimetric Weather Radar, Journal of Atmospheric and Oceanic Technology, 17(3), 332-356. Retrieved Nov 24, 2021, from https://journals.ametsoc.org/view/journals/atot/17/3/1520-0426_2000_017_0332_trpaat_2_0_co_2.xml\n",