Merge pull request #566 from GavinHuttley/develop

Simplifications for rtd builds
cogent3 · Mar 10, 2020 · 8995534 · 8995534
2 parents e4a6da7 + 72d7bd9
commit 8995534
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Showing 4 changed files with 32 additions and 34 deletions.
diff --git a/doc/rtd-environment.yml b/doc/rtd-environment.yml
@@ -3,30 +3,19 @@ channels:
   - conda-forge
   - plotly
 dependencies:
-  - nodejs
   - python=3.7
-  - pandoc
   - plotly
   - plotly-orca
   - pip
   - pip:
-    - numpy
     - numpydoc
-    - tqdm
-    - scitrack
-    - tinydb
-    - pandas
-    - jupyterlab
-    - jupyter_client
+    - psutil
     - ipython
     - ipykernel
     - ipywidgets
     - sphinx>=1.6
     - nbsphinx
     - nbformat
-    - jupyterlab
     - nbconvert!=5.4
-    - jupytext
     - sphinxcontrib-bibtex
-    - sphinx_rtd_theme
     - sphinx-gallery
diff --git a/setup.py b/setup.py
@@ -169,31 +169,32 @@ def CythonExtension(module_name, **kw):
     ],
     packages=find_packages(where="src"),
     package_dir={"": PACKAGE_DIR},
-    install_requires=["numpy", "pandas", "plotly", "scitrack", "tqdm", "tinydb"],
+    install_requires=["numpy", "plotly", "scitrack", "tqdm", "tinydb"],
     extras_require={
         "dev": [
-            "pytest-azurepipelines",
-            "jupyterlab",
+            "black",
+            "click",
+            "ipykernel",
             "ipykernel",
             "ipywidgets",
-            "click",
-            "sphinx",
-            "sphinx_rtd_theme",
-            "sphinx-autobuild",
-            "sphinxcontrib-bibtex",
-            "numpydoc",
-            "nbformat",
-            "nbconvert",
+            "isort",
             "jupyter_client",
-            "ipykernel",
-            "nbsphinx",
+            "jupyterlab",
             "jupytext",
-            "pytest",
+            "nbconvert",
+            "nbformat",
+            "nbsphinx",
+            "numpydoc",
+            "pandas",
+            "psutil",
+            "pytest-azurepipelines",
             "pytest-cov",
             "pytest>=4.3.0",
+            "sphinx",
+            "sphinx-autobuild",
+            "sphinx_rtd_theme",
+            "sphinxcontrib-bibtex",
             "tox",
-            "black",
-            "isort",
         ]
     },
     ext_modules=cythonize(

diff --git a/tests/test_util/test_table.py b/tests/test_util/test_table.py
@@ -7,15 +7,20 @@
 import pickle
 
 from tempfile import TemporaryDirectory
+from unittest import TestCase, main, skipIf
 
 import numpy
 
 from numpy.testing import assert_equal
-from pandas import DataFrame
 
 from cogent3 import load_table, make_table
 from cogent3.util.table import Table, cast_to_array, formatted_array
-from cogent3.util.unit_test import TestCase, main
+
+
+try:
+    from pandas import DataFrame
+except ImportError:
+    DataFrame = None
 
 
 __author__ = "Thomas La"
@@ -447,12 +452,13 @@ def test_dunder_repr_eq_str(self):
         r = repr(t)
         self.assertTrue(r.startswith(s))
 
+    @skipIf(DataFrame is None, "pandas not installed")
     def test_make_table_from_dataframe(self):
         """makes a table from a pandas data frame"""
         df = DataFrame(data=[[0, 1], [3, 7]], columns=["a", "b"])
         t = make_table(data_frame=df)
-        self.assertEqual(t.columns["a"], [0, 3])
-        self.assertEqual(t.columns["b"], [1, 7])
+        assert_equal(t.columns["a"], [0, 3])
+        assert_equal(t.columns["b"], [1, 7])
         with self.assertRaises(TypeError):
             make_table(data_frame="abcde")
 
@@ -753,10 +759,10 @@ def test_with_new_column(self):
         # now using a string expression
         t8 = Table(header=self.t8_header, data=self.t8_rows, row_ids="edge.name")
         n = t8.with_new_column("YZ", callback="y+z")
-        self.assertEqual(n.columns["YZ"], [9.0, 9.0])
+        assert_equal(n.columns["YZ"], [9.0, 9.0])
         # if the new column alreayb exists, the new table has the newest column
         n2 = t8.with_new_column("YZ", callback="y*z")
-        self.assertEqual(n2.columns["YZ"], [18.0, 18.0])
+        assert_equal(n2.columns["YZ"], [18.0, 18.0])
         self.assertNotEqual(id(n), id(n2))
         # bu the column arrays that have not changed should be equal
         for c in n.columns:
@@ -1031,6 +1037,7 @@ def test_tail(self):
         self.assertEqual(tail.data.tolist(), self.t1_rows[-3:])
         table.display = display
 
+    @skipIf(DataFrame is None, "pandas not installed")
     def test_to_dataframe(self):
         """produces a dataframe"""
         t = Table(header=self.t1_header, data=self.t1_rows)

diff --git a/tox.ini b/tox.ini
@@ -9,6 +9,7 @@ deps = numpy
        click
        pytest
        scitrack
+       pandas
        doctest: nbformat
        doctest: nbconvert
        doctest: jupyter_client