add zipped packages to Zenodo-upload

.gitignore

@@ -88,5 +88,8 @@ target/
 # Mypy cache
 .mypy_cache/
 
-# dask
-dask-worker-space
+# other
+dask-worker-space
+nb_logs
+.virtual_documents
+shared_gcs.py

HISTORY.rst

@@ -1,6 +1,11 @@
 History
 =======
 
+v1.1.2
+------
+* Update zenodo-upload.ipynb to include packages
+* Update readme to emphasize environment.yml
+
 v1.1.1
 ------
 * Update package dependencies

README.md

@@ -30,6 +30,7 @@ The requisite packages for executing the full Depsky et al. 2023 workflow are id
 
 ```bash
 mamba env create -f /path/to/environment.yml
+mamba activate pyciam
 ```
 
 ## Quickstart

environment/environment.yml

@@ -1,7 +1,6 @@
 name: pyciam
 channels:
   - conda-forge
-
 dependencies:
   - bottleneck=1.3
   - bokeh=2.4.3  # for use of dask dashboard

notebooks/post-processing/zenodo-upload.ipynb

@@ -4,7 +4,9 @@
    "cell_type": "code",
    "execution_count": 1,
    "id": "706cee66-6557-402d-ae97-679ed202a9fe",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import sys\n",
@@ -14,25 +16,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "id": "29a54dac-abdc-4a95-967f-2289fc1c9ecb",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/srv/conda/envs/notebook/lib/python3.9/site-packages/dask_gateway/client.py:21: FutureWarning: format_bytes is deprecated and will be removed in a future release. Please use dask.utils.format_bytes instead.\n",
-      "  from distributed.utils import LoopRunner, format_bytes\n"
-     ]
-    }
-   ],
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
    "source": [
     "import json\n",
     "from os import environ\n",
     "from pathlib import Path\n",
     "from shutil import make_archive\n",
     "from tempfile import TemporaryDirectory\n",
+    "from pathlib import Path\n",
     "\n",
     "import dask.config\n",
     "import requests\n",
@@ -45,12 +41,14 @@
    "cell_type": "code",
    "execution_count": 3,
    "id": "d37ca26f-091d-4cb6-be02-385464e0b687",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<dask.config.set at 0x7fb0070b1fd0>"
+       "<dask.config.set at 0x112a25b70>"
       ]
      },
      "execution_count": 3,
@@ -86,7 +84,9 @@
     "TITLES = {\n",
     "    \"SLIIDERS\": \"SLIIDERS: Sea Level Impacts Input Dataset by Elevation, Region, and Scenario\",\n",
     "    \"pyCIAM\": \"Estimates of Global Coastal Losses Under Multiple Sea Level Rise Scenarios\",\n",
-    "}"
+    "}\n",
+    "PYCIAM_CODE_PATH=Path(\"pyCIAM-1.1.2.zip\")\n",
+    "SLIIDERS_CODE_PATH=Path(\"sliiders-1.1.1.zip\")"
    ]
   },
   {
@@ -235,7 +235,12 @@
     "            shared.PATHS_SURGE_LOOKUP[\"seg_adm\"],\n",
     "        ],\n",
     "    },\n",
-    "}"
+    "}\n",
+    "\n",
+    "if PYCIAM_CODE_PATH is not None:\n",
+    "    ORIGINAL_PATHS[\"pyCIAM\"][\"source\"] = [PYCIAM_CODE_PATH]\n",
+    "if SLIIDERS_CODE_PATH is not None:\n",
+    "    ORIGINAL_PATHS[\"SLIIDERS\"][\"source\"] = [SLIIDERS_CODE_PATH"
    ]
   },
   {
@@ -434,15 +439,19 @@
     "    )\n",
     "    uploads[name] += upload_file_list(\n",
     "        this_dep, kind[\"products\"], \"products/\", overwrite=False\n",
-    "    )"
+    "    )\n",
+    "    if \"source\" in kind.keys(): \n",
+    "        uploads[name] += upload_file_list(\n",
+    "            this_dep, kind[\"source\"], \"source/\", overwrite=False\n",
+    "        )"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python [conda env:sliiders]",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-sliiders-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -454,7 +463,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.10"
+   "version": "3.10.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {