HARMONY-1909: Fix make build.

.readthedocs.yaml

@@ -15,7 +15,10 @@ build:
 sphinx:
    configuration: docs/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
+# Install Python dependencies using pyproject.toml
 python:
    install:
-   - requirements: requirements/docs.txt
+     - method: pip
+       path: .
+       extra_requirements:
+         - docs

Makefile

@@ -15,10 +15,11 @@ clean-docs:
 
 install:
 	python -m pip install --upgrade pip
-	pip install -r requirements/core.txt -r requirements/dev.txt -r requirements/docs.txt
+	pip install .
+	pip install .[dev,docs]
 
 install-examples: install
-	pip install -r requirements/examples.txt
+	pip install .[examples]
 
 examples: install-examples
 	jupyter-lab

docs/user/notebook.html

@@ -7495,20 +7495,20 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-InputPrompt jp-InputArea-prompt">In [1]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span><span class="p">;</span> <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'..'</span><span class="p">)</span>
-<span class="o">!{</span>sys.executable<span class="o">}</span><span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-q<span class="w"> </span>-r<span class="w"> </span>../requirements/examples.txt
+<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">helper</span>
 
-<span class="c1"># Install harmony-py requirements.  Not necessary if you ran `pip install harmony-py` in your kernel</span>
-<span class="o">!{</span>sys.executable<span class="o">}</span><span class="w"> </span>-m<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-q<span class="w"> </span>-r<span class="w"> </span>../requirements/core.txt
+<span class="c1"># Install the project with both 'examples' and 'dev' extra dependencies</span>
+<span class="n">helper</span><span class="o">.</span><span class="n">install_project_and_dependencies</span><span class="p">(</span><span class="s1">'..'</span><span class="p">,</span> <span class="n">libs</span><span class="o">=</span><span class="p">[</span><span class="s1">'examples'</span><span class="p">])</span>
 
+<span class="kn">import</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">datetime</span> <span class="k">as</span> <span class="nn">dt</span>
 <span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">display</span><span class="p">,</span> <span class="n">JSON</span>
 <span class="kn">import</span> <span class="nn">rasterio</span>
 <span class="kn">import</span> <span class="nn">rasterio.plot</span>
 <span class="kn">import</span> <span class="nn">netCDF4</span> <span class="k">as</span> <span class="nn">nc4</span>
 <span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">import</span> <span class="nn">helper</span>
+
 
 <span class="kn">from</span> <span class="nn">harmony</span> <span class="kn">import</span> <span class="n">BBox</span><span class="p">,</span> <span class="n">WKT</span><span class="p">,</span> <span class="n">Client</span><span class="p">,</span> <span class="n">Collection</span><span class="p">,</span> <span class="n">Request</span><span class="p">,</span> <span class="n">Environment</span>
 </pre></div>
@@ -7719,7 +7719,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856803_2020_01_01_7f00ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857426_2020_01_01_7f00ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7732,7 +7732,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856804_2020_01_01_7f00ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857427_2020_01_01_7f00ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7745,7 +7745,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856805_2020_01_02_3200ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857428_2020_01_02_3200ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7758,7 +7758,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856806_2020_01_03_0019ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857429_2020_01_03_0019ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7771,7 +7771,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856807_2020_01_04_0065ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857430_2020_01_04_0065ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7784,7 +7784,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856808_2020_01_05_00b2ff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857431_2020_01_05_00b2ff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7797,7 +7797,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856809_2020_01_06_00feff_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857432_2020_01_06_00feff_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7810,7 +7810,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856810_2020_01_07_00ffb2_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857433_2020_01_07_00ffb2_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7823,7 +7823,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856811_2020_01_08_00ff66_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857434_2020_01_08_00ff66_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -7836,7 +7836,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child">
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
-<pre>/tmp/4856812_2020_01_09_00ff19_global_blue_var_regridded_subsetted.tif
+<pre>/tmp/4857435_2020_01_09_00ff19_global_blue_var_regridded_subsetted.tif
 </pre>
 </div>
 </div>
@@ -8009,7 +8009,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child jp-OutputArea-executeResult">
 <div class="jp-OutputPrompt jp-OutputArea-prompt">Out[11]:</div>
 <div class="jp-RenderedText jp-OutputArea-output jp-OutputArea-executeResult" data-mime-type="text/plain" tabindex="0">
-<pre>&lt;matplotlib.image.AxesImage at 0x1271cefd0&gt;</pre>
+<pre>&lt;matplotlib.image.AxesImage at 0x12cde2d50&gt;</pre>
 </div>
 </div>
 <div class="jp-OutputArea-child">
@@ -8060,7 +8060,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child jp-OutputArea-executeResult">
 <div class="jp-OutputPrompt jp-OutputArea-prompt">Out[12]:</div>
 <div class="jp-RenderedText jp-OutputArea-output jp-OutputArea-executeResult" data-mime-type="text/plain" tabindex="0">
-<pre>'3d9ff057-50af-430b-bc9c-8edd13430078'</pre>
+<pre>'d5306445-54aa-4457-bf3c-9fca9d4e50e1'</pre>
 </div>
 </div>
 </div>
@@ -8192,7 +8192,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputArea-child jp-OutputArea-executeResult">
 <div class="jp-OutputPrompt jp-OutputArea-prompt">Out[15]:</div>
 <div class="jp-RenderedText jp-OutputArea-output jp-OutputArea-executeResult" data-mime-type="text/plain" tabindex="0">
-<pre>'b049d8f3-6fea-439b-aad6-60da59dcf1f7'</pre>
+<pre>'91b2043e-2bf2-444a-a47a-15f0247a380a'</pre>
 </div>
 </div>
 </div>
@@ -8232,7 +8232,7 @@ <h2 id="Harmony-Py-Tutorial">Harmony Py Tutorial<a class="anchor-link" href="#Ha
 <div class="jp-OutputPrompt jp-OutputArea-prompt"></div>
 <div class="jp-RenderedText jp-OutputArea-output" data-mime-type="text/plain" tabindex="0">
 <pre>
-  /tmp/4856817_001_00_7f00ff_global_blue_var_regridded.nc.png
+  /tmp/4857440_001_00_7f00ff_global_blue_var_regridded.nc.png
 </pre>
 </div>
 </div>

examples/helper.py

@@ -1,17 +1,33 @@
 import sys
-sys.path.append('..')
-
-import datetime as dt
-from getpass import getpass
-from glob import glob
-from time import sleep
-
-import ipyplot
-from ipywidgets import IntSlider, Password, Text
-from IPython.display import display, JSON
+import os
 import rasterio
 from rasterio.plot import show
-import requests
+
+def install_project_and_dependencies(project_root, libs=None):
+    """
+    Change to the project root, install the project and its optional dependencies,
+    then switch back to the original directory.
+
+    :param project_root: Path to the project root directory where pyproject.toml or setup.py is located.
+    :param libs: List of optional pip extra dependencies (e.g., ['examples', 'dev']).
+    """
+    # Save the current working directory
+    original_dir = os.getcwd()
+
+    try:
+        # Change directory to the project root
+        os.chdir(project_root)
+
+        # If libs are specified, install them
+        if libs:
+            libs_str = ','.join(libs)
+            os.system(f'{sys.executable} -m pip install -q .[{libs_str}]')
+
+        # Install the project itself
+        os.system(f'{sys.executable} -m pip install -q .')
+    finally:
+        # Switch back to the original directory after installation
+        os.chdir(original_dir)
 
 
 def show_result(filename):

examples/tutorial.ipynb

@@ -21,20 +21,20 @@
    },
    "outputs": [],
    "source": [
-    "import sys; sys.path.append('..')\n",
-    "!{sys.executable} -m pip install -q -r ../requirements/examples.txt\n",
+    "import helper\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",
+    "# Install the project and 'examples' dependencies\n",
+    "helper.install_project_and_dependencies('..', libs=['examples'])\n",
     "\n",
+    "import sys\n",
     "import datetime as dt\n",
     "from IPython.display import display, JSON\n",
     "import rasterio\n",
     "import rasterio.plot\n",
     "import netCDF4 as nc4\n",
     "from matplotlib import pyplot as plt\n",
     "import numpy as np\n",
-    "import helper\n",
+    "\n",
     "\n",
     "from harmony import BBox, WKT, Client, Collection, Request, Environment"
    ]

pyproject.toml

@@ -26,20 +26,57 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3 :: Only",
 ]
-dynamic = ["dependencies", "optional-dependencies", "version"]
+dynamic = ["version"]
+dependencies = [
+    "python-dateutil ~= 2.8.2",
+    "python-dotenv ~= 0.20.0",
+    "progressbar2 ~= 4.2.0",
+    "requests ~= 2.32.3",
+    "sphinxcontrib-napoleon ~= 0.7",
+    "curlify ~= 2.2.1",
+    "shapely ~= 2.0.4"
+]
 
 [project.urls]
 Homepage = "https://github.com/nasa/harmony-py"
 Documentation = "https://harmony-py.readthedocs.io/en/main/"
 Repository = "https://github.com/nasa/harmony-py.git"
 
-[project.dependencies]
-dependencies = ["-r requirements/core.txt"]
-
 [project.optional-dependencies]
-dev = ["-r requirements/dev.txt"]
-docs = ["-r requirements/docs.txt"]
-examples = ["-r requirements/examples.txt"]
+dev = [
+    "coverage ~= 5.4",
+    "flake8 ~= 7.1.1",
+    "hypothesis ~= 6.2",
+    "PyYAML ~= 6.0.1",
+    "pytest ~= 6.2",
+    "pytest-cov ~= 2.11",
+    "pytest-mock ~= 3.5",
+    "pytest-watch ~= 4.2",
+    "responses ~= 0.25.3"
+]
+docs = [
+    "curlify ~= 2.2.1",
+    "Jinja2 ~= 3.1.2",
+    "load-dotenv ~=0.1.0",
+    "nbconvert ~= 7.10.0",
+    "progressbar2 ~= 4.2.0",
+    "sphinx ~= 7.1.2",
+    "sphinx-rtd-theme ~= 1.3.0",
+    "shapely ~= 2.0.4"
+]
+examples = [
+    "boto3 ~= 1.28",
+    "intake-stac ~= 0.4.0",
+    "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"
+]
 
 [tool.setuptools.dynamic]
 # Will read __version__ from harmony.__init__.py
@@ -48,12 +85,6 @@ version = {attr = "harmony.__version__"}
 [tool.setuptools.packages.find]
 exclude = ["contrib", "docs", "tests*"]
 
-[tool.setuptools]
-include_package_data = true
-
-[tool.setuptools.test]
-test_suite = "tests"
-
 [tool.flake8]
 max-line-length = 99
 ignore = ["F401", "W503"]