Mitigate Snyk vulnerabilities in documentation dependencies.

nasa · Nov 1, 2023 · a006894 · a006894
1 parent 854522e
commit a006894
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ We welcome feedback on Harmony-Py via [GitHub Issues](https://github.com/nasa/ha
 
 ## Prerequisites
 
-* Python 3.7+
+* Python 3.8+
 
 
 ## Installing

diff --git a/examples/basic.ipynb b/examples/basic.ipynb
@@ -108,7 +108,8 @@
     "\n",
     "request = Request(\n",
     "    collection=collection,\n",
-    "    spatial=BBox(-165, 52, -140, 77)\n",
+    "    spatial=BBox(-165, 52, -140, 77),\n",
+    "    format='image/tiff'\n",
     ")"
    ]
   },
@@ -167,15 +168,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f'\\n{job1_id}')\n",
+    "print(f'\\nHarmony job ID: {job1_id}')\n",
     "\n",
     "print('\\nWaiting for the job to finish')\n",
     "results = harmony_client.result_json(job1_id, show_progress=True)\n",
     "\n",
     "print('\\nDownloading results:')\n",
     "futures = harmony_client.download_all(job1_id)\n",
+    "\n",
     "for f in futures:\n",
     "    print(f.result())  # f.result() is a filename, in this case\n",
+    "\n",
     "print('\\nDone downloading.')"
    ]
   },
@@ -194,9 +197,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "futures = harmony_client.download_all(job1_id, overwrite=False)\n",
     "filenames = [f.result() for f in futures]\n",
+    "\n",
     "for filename in filenames:\n",
     "    helper.show_result(filename)"
    ]
@@ -221,7 +224,9 @@
     "    temporal={\n",
     "        'start': dt.datetime(2020, 6, 1),\n",
     "        'stop': dt.datetime(2020, 6, 30)\n",
-    "    })\n",
+    "    },\n",
+    "    format='image/tiff'\n",
+    ")\n",
     "\n",
     "job2_id = harmony_client.submit(request)"
    ]
@@ -268,7 +273,9 @@
     "    temporal={\n",
     "        'start': dt.datetime(2010, 1, 1),\n",
     "        'stop': dt.datetime(2020, 12, 30)\n",
-    "    })\n",
+    "    },\n",
+    "    format='image/tiff'\n",
+    ")\n",
     "\n",
     "job3_id = harmony_client.submit(request)"
    ]
@@ -339,12 +346,14 @@
     "\n",
     "request = Request(\n",
     "    collection=collection,\n",
-    "    spatial=BBox(-183, 40, 10, 30)\n",
+    "    spatial=BBox(-183, 40, 10, 30),\n",
+    "    format='image/tiff'\n",
     ")\n",
     "\n",
-    "print(f\"Request valid? {request.is_valid()}\")\n",
+    "print(f'Request valid? {request.is_valid()}')\n",
+    "\n",
     "for m in request.error_messages():\n",
-    "    print(\" * \" + m)"
+    "    print(f' * {m}')"
    ]
   },
   {
@@ -369,12 +378,14 @@
     "    temporal={\n",
     "        'start': dt.datetime(2020, 12, 30),\n",
     "        'stop': dt.datetime(2010, 1, 1)\n",
-    "    }\n",
+    "    },\n",
+    "    format='image/tiff'\n",
     ")\n",
     "\n",
-    "print(f\"Request valid? {request.is_valid()}\")\n",
+    "print(f'Request valid? {request.is_valid()}')\n",
+    "\n",
     "for m in request.error_messages():\n",
-    "    print(\" * \" + m)"
+    "    print(f' * {m}')"
    ]
   },
   {
@@ -400,12 +411,14 @@
     "    temporal={\n",
     "        'start': dt.datetime(2020, 12, 30),\n",
     "        'stop': dt.datetime(2010, 1, 1)\n",
-    "    }\n",
+    "    },\n",
+    "    format='image/tiff'\n",
     ")\n",
     "\n",
-    "print(f\"Request valid? {request.is_valid()}\")\n",
+    "print(f'Request valid? {request.is_valid()}')\n",
+    "\n",
     "for m in request.error_messages():\n",
-    "    print(\" * \" + m)"
+    "    print(f' * {m}')"
    ]
   },
   {
@@ -426,7 +439,7 @@
     "try:\n",
     "    harmony_client.submit(request)\n",
     "except Exception as e:\n",
-    "    print(\"Harmony Py raised an exception:\\n\")\n",
+    "    print('Harmony Py raised an exception:\\n')\n",
     "    print(e)"
    ]
   },
@@ -456,7 +469,8 @@
     "        'start': dt.datetime(2021, 1, 1),\n",
     "        'stop': dt.datetime(2021, 1, 10)\n",
     "    },\n",
-    "    max_results=2\n",
+    "    max_results=2,\n",
+    "    format='image/tiff'\n",
     ")\n",
     "request.is_valid()"
    ]
@@ -498,6 +512,7 @@
    "outputs": [],
    "source": [
     "job_id = harmony_client.submit(request)\n",
+    "\n",
     "for filename in [f.result() for f in harmony_client.download_all(job_id)]:\n",
     "    helper.show_result(filename)"
    ]
@@ -630,14 +645,6 @@
     "for filename in [f.result() for f in harmony_client.download_all(job_id)]:\n",
     "    helper.show_result(filename)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "cd883298-4642-4128-baff-e4291fb4d00d",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -656,7 +663,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {

diff --git a/examples/job_stac.ipynb b/examples/job_stac.ipynb
@@ -16,12 +16,13 @@
    "source": [
     "import sys\n",
     "sys.path.append('..')\n",
+    "\n",
     "!{sys.executable} -m pip install -q -r ../requirements/examples.txt\n",
     "\n",
     "# Install harmony-py requirements.  Not necessary if you ran `pip install harmony-py` in your kernel  \n",
     "!{sys.executable} -m pip install -q -r ../requirements/core.txt\n",
     "\n",
-    "from harmony import BBox, Client, Collection, Request, Environment\n"
+    "from harmony import BBox, Client, Collection, Request, Environment"
    ]
   },
   {
@@ -37,7 +38,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "    harmony_client = Client(env=Environment.UAT)  # assumes .netrc usage\n",
+    "harmony_client = Client(env=Environment.UAT)  # assumes .netrc usage\n",
     "\n",
     "collection = Collection(id='C1234088182-EEDTEST')\n",
     "request = Request(\n",
@@ -47,7 +48,7 @@
     ")\n",
     "\n",
     "job_id = harmony_client.submit(request)\n",
-    "job_id\n"
+    "job_id"
    ]
   },
   {
@@ -63,7 +64,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "stac_catalog_url = harmony_client.stac_catalog_url(job_id, show_progress=True)\n"
+    "stac_catalog_url = harmony_client.stac_catalog_url(job_id, show_progress=True)"
    ]
   },
   {
@@ -81,16 +82,17 @@
    "source": [
     "from urllib.parse import urlparse\n",
     "import requests\n",
-    "from pystac import STAC_IO\n",
+    "from pystac import stac_io\n",
+    "\n",
     "\n",
     "def requests_read_method(uri):\n",
     "    parsed = urlparse(uri)\n",
     "    if parsed.hostname.startswith('harmony.') or parsed.hostname.startswith('localhost'):\n",
     "        return harmony_client.read_text(uri)\n",
     "    else:\n",
-    "        return STAC_IO.default_read_text_method(uri)\n",
+    "        return stac_io.default_read_text_method(uri)\n",
     "\n",
-    "STAC_IO.read_text_method = requests_read_method"
+    "stac_io.read_text_method = requests_read_method"
    ]
   },
   {
@@ -107,19 +109,14 @@
    "outputs": [],
    "source": [
     "from pystac import Catalog\n",
-    "cat = Catalog.from_file(stac_catalog_url)\n",
     "\n",
+    "\n",
+    "cat = Catalog.from_file(stac_catalog_url)\n",
     "print(cat.title)\n",
+    "\n",
     "for item in cat.get_all_items():\n",
     "    print(item.datetime, item.properties.get('expires'), [asset.href for asset in item.assets.values()])"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -138,7 +135,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/harmony/harmony.py b/harmony/harmony.py
@@ -1187,14 +1187,16 @@ def iterator(
         Each iteration returns a dictionary, or `None` when all granules have been iterated.
         The dictionary has the following form:
 
-        {
-            'path': Future
-            'bbox': BBox object containing the bounding box for the granule,
-            'temporal': {
-                'start': '2020-01-11T14:00:00.000Z',
-                'end': '2020-01-11T15:59:59.000Z'
+        .. code-block:: python
+
+            {
+                'path': Future
+                'bbox': BBox object containing the bounding box for the granule,
+                'temporal': {
+                    'start': '2020-01-11T14:00:00.000Z',
+                    'end': '2020-01-11T15:59:59.000Z'
+                }
             }
-        }
 
         The Future resolves to the path to the downloaded file.
 

diff --git a/requirements/core.txt b/requirements/core.txt
@@ -1,6 +1,6 @@
 python-dateutil ~= 2.8.2
 python-dotenv ~= 0.20.0
-progressbar2 ~= 3.55.0
+progressbar2 ~= 4.2.0
 requests ~= 2.28
 sphinxcontrib-napoleon ~= 0.7
 curlify ~= 2.2.1
diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -13,5 +13,5 @@ pytest-mock ~= 3.5
 pytest-watch ~= 4.2
 responses ~= 0.12
 setuptools >= 54.2
-sphinx ~= 5.3.0
+sphinx ~= 7.1.2
 wheel >= 0.36
diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -1,7 +1,7 @@
-nbconvert ~= 7.4.0
+curlify ~= 2.2.1
 Jinja2 ~= 3.1.2
 load-dotenv ~=0.1.0
-curlify ~= 2.2.1
-progressbar2 ~= 3.55.0
-sphinx ~= 5.3.0
-sphinx-rtd-theme ~= 1.2.0
+nbconvert ~= 7.10.0
+progressbar2 ~= 4.2.0
+sphinx ~= 7.1.2
+sphinx-rtd-theme ~= 1.3.0
diff --git a/requirements/examples.txt b/requirements/examples.txt
@@ -1,10 +1,11 @@
-boto3 ~= 1.17
-ipyplot ~= 1.1
-ipywidgets ~= 7.6
-jupyterlab ~= 3.0
-matplotlib ~= 3.3
-pystac ~= 1.7.3
-rasterio ~= 1.2
+boto3 ~= 1.28
 intake-stac ~= 0.4.0
-netCDF4
-numpy
+ipyplot ~= 1.1
+ipywidgets ~= 8.1
+jupyterlab ~= 4.0
+matplotlib ~= 3.8
+netCDF4 ~= 1.6
+numpy ~= 1.26
+pillow ~= 10.1  # A dependency of ipyplot, pinned to avoid critical vulnerability.
+pystac ~= 1.9.0
+rasterio ~= 1.3