Merge pull request #152 from ocefpaf/install_missing_colab

add hidden cell to install colab missing deps
ioos · Sep 1, 2023 · cb0082a · cb0082a
2 parents a615c54 + fe955a3
commit cb0082a
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: double-quote-string-fixer
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0
+    rev: v3.0.3
     hooks:
       - id: prettier
         types_or: [html]
@@ -30,12 +30,12 @@ repos:
         language_version: python3
 
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v3.0.1
+    rev: v3.1.0
     hooks:
       - id: add-trailing-comma
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.281
+    rev: v0.0.287
     hooks:
       - id: ruff
 

diff --git a/jupyterbook/content/code_gallery/data_access_notebooks/2016-10-12-fetching_data.ipynb b/jupyterbook/content/code_gallery/data_access_notebooks/2016-10-12-fetching_data.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"erddapy\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/jupyterbook/content/code_gallery/data_access_notebooks/2016-11-15-glider_data_example.ipynb b/jupyterbook/content/code_gallery/data_access_notebooks/2016-11-15-glider_data_example.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"cf_xarray\", \"palettable\", \"seawater\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/.../content/code_gallery/data_access_notebooks/2016-12-20-searching_glider_deployments.ipynb b/.../content/code_gallery/data_access_notebooks/2016-12-20-searching_glider_deployments.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"iris\", \"seawater\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/...ntent/code_gallery/data_access_notebooks/2017-01-18-siphon-explore-thredds.archived.ipynb b/...ntent/code_gallery/data_access_notebooks/2017-01-18-siphon-explore-thredds.archived.ipynb
@@ -52,17 +52,15 @@
     "catalog = TDSCatalog(\"https://thredds.cencoos.org/thredds/catalog.xml\")\n",
     "\n",
     "\n",
-    "info = \"\"\"\n",
+    "info = f\"\"\"\n",
     "Catalog information\n",
     "-------------------\n",
     "\n",
-    "Base THREDDS URL: {}\n",
-    "Catalog name: {}\n",
-    "Catalog URL: {}\n",
-    "Metadata: {}\n",
-    "\"\"\".format(\n",
-    "    catalog.base_tds_url, catalog.catalog_name, catalog.catalog_url, catalog.metadata\n",
-    ")\n",
+    "Base THREDDS URL: {catalog.base_tds_url}\n",
+    "Catalog name: {catalog.catalog_name}\n",
+    "Catalog URL: {catalog.catalog_url}\n",
+    "Metadata: {catalog.metadata}\n",
+    "\"\"\"\n",
     "\n",
     "print(info)"
    ]
@@ -234,13 +232,11 @@
     }
    ],
    "source": [
-    "info = \"\"\"\n",
-    "Href: {}\n",
-    "Name: {}\n",
-    "Title: {}\n",
-    "\"\"\".format(\n",
-    "    ref.href, ref.name, ref.title\n",
-    ")\n",
+    "info = f\"\"\"\n",
+    "Href: {ref.href}\n",
+    "Name: {ref.name}\n",
+    "Title: {ref.title}\n",
+    "\"\"\"\n",
     "\n",
     "print(info)"
    ]

diff --git a/...erbook/content/code_gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb b/...erbook/content/code_gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"erddapy\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/...rbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb b/...rbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"owslib\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -113,10 +153,8 @@
     "        \"SCCOOS\": \"Southern California Coastal Ocean Observing System\",\n",
     "        \"SECOORA\": \"Southeast Coastal Ocean Observing Regional Association\",\n",
     "    }\n",
-    "    reg_assoc = '(dataThemeinstitutions_s:\"{}\" dataThemeprojects_s:\"{} ({})\")'.format(\n",
-    "        RAs[ra],\n",
-    "        RAs[ra],\n",
-    "        ra,\n",
+    "    reg_assoc = (\n",
+    "        f'(dataThemeinstitutions_s:\"{RAs[ra]}\" dataThemeprojects_s:\"{RAs[ra]} ({ra})\")'\n",
     "    )\n",
     "\n",
     "# Identify the project.\n",

diff --git a/jupyterbook/content/code_gallery/data_access_notebooks/2017-09-09-hurricane_irma.ipynb b/jupyterbook/content/code_gallery/data_access_notebooks/2017-09-09-hurricane_irma.ipynb
@@ -1,5 +1,45 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "import sys\n",
+    "\n",
+    "COLAB = \"google.colab\" in sys.modules\n",
+    "\n",
+    "\n",
+    "def _install(package):\n",
+    "    if COLAB:\n",
+    "        ans = input(f\"Install { package }? [y/n]:\")\n",
+    "        if ans.lower() in [\"y\", \"yes\"]:\n",
+    "            subprocess.check_call(\n",
+    "                [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n",
+    "            )\n",
+    "            print(f\"{ package } installed!\")\n",
+    "\n",
+    "\n",
+    "def _colab_install_missing_deps(deps):\n",
+    "    import importlib\n",
+    "\n",
+    "    for dep in deps:\n",
+    "        if importlib.util.find_spec(dep) is None:\n",
+    "            if dep == \"iris\":\n",
+    "                dep = \"scitools-iris\"\n",
+    "            _install(dep)\n",
+    "\n",
+    "\n",
+    "deps = [\"cf-units\", \"ioos-tools\", \"pyoos\", \"retrying\"]\n",
+    "_colab_install_missing_deps(deps)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -46,7 +86,7 @@
    },
    "outputs": [],
    "source": [
-    "import sys\n",
+    "import sys  # noqa\n",
     "from pathlib import Path\n",
     "from urllib.request import urlopen, urlretrieve\n",
     "\n",
@@ -6518,7 +6558,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,