Tests fixes and contributor docs #952

Demetrio92 · 2018-09-04T18:49:04Z

While I was working on another PR, I noticed that few things are missing in the repository so a contributor is able to set up the dev enviroment. I did cost me quite some time to figure them all out, so here is a PR collecting them all.

…an enormous and complex traceback. see: vega/altair#972

…ake it a proper link

Conengmo

Thanks for this @Demetrio92! This type of PR can really help other users, I'm all for making it easier for people to contribute. Also good catch on the missing packages in requirements-dev, though I couldn't find where two of them are used. I placed some comments, I hope you have time to reply.

Conengmo · 2018-09-04T20:03:33Z

.github/CONTRIBUTING.md

-  5. Commit those changes
+  5. Make sure the tests pass:
+    * in the repository folder do `pip install -e .`  (needed for notebook tests)
+    * along with all the dependencies install `phantomjs` via `npm install -g phantomjs`


I don't have npm, I think I got phantomjs from phantomjs.org. Maybe say the npm part as hint, or tell people how to get npm.

see new commits

Conengmo · 2018-09-04T20:07:22Z

examples/Features.ipynb

+    "\n",
+    "try: \n",
+    "    from altair import Chart, load_dataset\n",
+    "except TypeError:\n",


Does altair raise a TypeError on older versions? Seems weird. If altair really doesn't work on older Python version, it should raise a deprecation warning or exception. Can you tell what error you encountered?

which is what i told them...
vega/altair#972 (comment)
(check the link for the type of error I've gotten)

Apparently Python is partially responsible for the error, so it's complicated...

Conengmo · 2018-09-04T20:09:49Z

requirements-dev.txt

@@ -1,5 +1,6 @@
 altair
 cartopy
+descartes


I couldn't find descartes, do you know where it was used?

tl;dr it's b/c geopandas do no handle dependencies properly, but essentially it breaks
TestNotebooks.test_time_slider_choropleth

Full traceback

_______________________________________ TestNotebooks.test_time_slider_choropleth _______________________________________ self = <test_notebooks.NotebookTester object at 0x7f755a854e48>, exporter = None, filename = None def __call__(self, exporter=None, filename=None): raw_nb = nbconvert.exporters.Exporter().from_filename(self.filename) raw_nb[0].metadata.setdefault('kernelspec', {})['name'] = 'python' > exec_nb = nbconvert.preprocessors.ExecutePreprocessor(timeout=600).preprocess(*raw_nb) tests/notebooks/test_notebooks.py:29: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ venv/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262: in preprocess nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) venv/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: in preprocess nb.cells[index], resources = self.preprocess_cell(cell, resources, index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f7556331eb8> cell = {'execution_count': 3, 'outputs': [{'ename': 'ImportError', 'output_type': 'error', 'evalue': 'The descartes package i...d': 'light'}}], 'source': '%matplotlib inline\n\nax = gdf.plot(figsize=(10, 10))', 'cell_type': 'code', 'metadata': {}} resources = defaultdict(None, {'output_extension': '.txt', 'metadata': defaultdict(None, {'name': 'TimeSliderChoropleth', 'path': '/home/demetrio/Parkbob/git/folium/tests/notebooks/../../examples', 'modified_date': 'September 3, 2018'})}) cell_index = 3 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code': return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs if not self.allow_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E %matplotlib inline E E ax = gdf.plot(figsize=(10, 10)) E ------------------ E E --------------------------------------------------------------------------- E ImportError Traceback (most recent call last) E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/geopandas/plotting.py in plot_polygon_collection(ax, geoms, values, color, cmap, vmin, vmax, **kwargs) E 81 try: E ---> 82 from descartes.patch import PolygonPatch E 83 except ImportError: E E ImportError: No module named 'descartes' E E During handling of the above exception, another exception occurred: E E ImportError Traceback (most recent call last) E <ipython-input-3-423c72b95e2e> in <module>() E 1 get_ipython().run_line_magic('matplotlib', 'inline') E 2 E ----> 3 ax = gdf.plot(figsize=(10, 10)) E E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/geopandas/geodataframe.py in plot(self, *args, **kwargs) E 532 from there. E 533 """ E --> 534 return plot_dataframe(self, *args, **kwargs) E 535 E 536 plot.__doc__ = plot_dataframe.__doc__ E E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/geopandas/plotting.py in plot_dataframe(df, column, cmap, color, ax, categorical, legend, scheme, k, vmin, vmax, markersize, figsize, legend_kwds, **style_kwds) E 412 return plot_series(df.geometry, cmap=cmap, color=color, ax=ax, E 413 figsize=figsize, markersize=markersize, E --> 414 **style_kwds) E 415 E 416 # To accept pd.Series and np.arrays as column E E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/geopandas/plotting.py in plot_series(s, cmap, color, ax, figsize, **style_kwds) E 292 values_ = values[poly_idx] if cmap else None E 293 plot_polygon_collection(ax, polys, values_, facecolor=facecolor, E --> 294 cmap=cmap, **style_kwds) E 295 E 296 # plot all LineStrings and MultiLineString components in same collection E E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/geopandas/plotting.py in plot_polygon_collection(ax, geoms, values, color, cmap, vmin, vmax, **kwargs) E 82 from descartes.patch import PolygonPatch E 83 except ImportError: E ---> 84 raise ImportError("The descartes package is required" E 85 " for plotting polygons in geopandas.") E 86 from matplotlib.collections import PatchCollection E E ImportError: The descartes package is required for plotting polygons in geopandas. E ImportError: The descartes package is required for plotting polygons in geopandas. venv/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError

Conengmo · 2018-09-04T20:10:16Z

requirements-dev.txt

@@ -20,7 +22,9 @@ pillow
 pycodestyle
 pytest
 selenium
+scipy


Same for scipy

tl;dr it's b/c of cartopy not handling dependencies properly, but essentially it breaks
TestNotebooks.test_geodedetic_image_overlay

full traceback

______________________________________ TestNotebooks.test_geodedetic_image_overlay ______________________________________ self = <test_notebooks.NotebookTester object at 0x7f13471bfd30>, exporter = None, filename = None def __call__(self, exporter=None, filename=None): raw_nb = nbconvert.exporters.Exporter().from_filename(self.filename) raw_nb[0].metadata.setdefault('kernelspec', {})['name'] = 'python' > exec_nb = nbconvert.preprocessors.ExecutePreprocessor(timeout=600).preprocess(*raw_nb) tests/notebooks/test_notebooks.py:29: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ venv/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262: in preprocess nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) venv/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: in preprocess nb.cells[index], resources = self.preprocess_cell(cell, resources, index) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f134398beb8> cell = {'execution_count': 6, 'source': "import cartopy.crs as ccrs\nfrom cartopy.img_transform import warp_array\n\nsource_e... 'scipy'"], 'ename': 'ImportError', 'output_type': 'error', 'evalue': "No module named 'scipy'"}], 'cell_type': 'code'} resources = defaultdict(None, {'metadata': defaultdict(None, {'name': 'GeodedeticImageOverlay', 'path': '/home/demetrio/Parkbob/git/folium/tests/notebooks/../../examples', 'modified_date': 'September 3, 2018'}), 'output_extension': '.txt'}) cell_index = 8 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code': return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs if not self.allow_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E import cartopy.crs as ccrs E from cartopy.img_transform import warp_array E E source_extent = [lon.min(), lon.max(), lat.min(), lat.max()] E E new_data = warp_array(colored_data, E target_proj=ccrs.GOOGLE_MERCATOR, E source_proj=ccrs.PlateCarree(), E target_res=data.shape, E source_extent=source_extent, E target_extent=None, E mask_extrapolated=False) E E E m = folium.Map(location=[lat.mean(), lon.mean()], zoom_start=1) E E folium.raster_layers.ImageOverlay( E image=new_data[0], E bounds=[[lat.min(), lon.min()], [lat.max(), lon.max()]], E opacity=0.25 E ).add_to(m) E E m.save(os.path.join('results', 'GeodedeticImageOverlay_2.html')) E E m E ------------------ E E --------------------------------------------------------------------------- E ImportError Traceback (most recent call last) E <ipython-input-6-f0b9096a59bd> in <module>() E 1 import cartopy.crs as ccrs E ----> 2 from cartopy.img_transform import warp_array E 3 E 4 source_extent = [lon.min(), lon.max(), lat.min(), lat.max()] E 5 E E ~/Parkbob/git/folium/venv/lib/python3.5/site-packages/cartopy/img_transform.py in <module>() E 24 E 25 import numpy as np E ---> 26 import scipy.spatial E 27 E 28 import cartopy.crs as ccrs E E ImportError: No module named 'scipy' E ImportError: No module named 'scipy' venv/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError

they already know that: SciTools/cartopy#1112

Conengmo · 2018-09-04T20:11:27Z

README.rst

+Contributing
+------------
+
+see `.github/CONTRIBUTING.md`


Maybe we could add one or two lines here so it's a bit more welcoming. Something about how folium is maintained by volunteers, that contributions are welcome, and that people should check the issues.

Sure, i will, you're right!
Can you help me with the link? I tried .. _relative_link but it seems to only work as rst-to-rst :(

see new commits

Demetrio92 · 2018-09-04T21:22:43Z

@Conengmo i guess we have a small timezone issue here. Please let both of my PRs sit here for a few days, i will address all the comments

python-visualization#952 (comment)

Demetrio92 · 2018-09-05T17:49:17Z

I think I addressed all the issues, let me know if anything still remains.
@Conengmo

Complete link to the contributors guide. Also updated the documentation version.

Screwed up the documentation links :(

Conengmo · 2018-09-28T10:58:42Z

Thanks for helping out @Demetrio92!

Demetrio92 added 4 commits September 4, 2018 20:41

add missing packages to the requirements

3f68209

add explanation on how to run the tests

cd4580d

handle altair error which is due to python typing issue, but creates …

c93e61a

…an enormous and complex traceback. see: vega/altair#972

add reference to the contributors guidlines into the readme. FIXME: m…

567d981

…ake it a proper link

Demetrio92 mentioned this pull request Sep 4, 2018

show_in_browser() method for folium.folium.Map #953

Closed

Conengmo reviewed Sep 4, 2018

View reviewed changes

Demetrio92 added 2 commits September 5, 2018 19:37

addressing python-visualization#952 (comment)

7fb015b

more welcoming contributors message. Stolen from .github/CONRIBUTING.md

d83beff

python-visualization#952 (comment)

Conengmo added 3 commits September 28, 2018 11:37

Update README.rst

3ef583a

Complete link to the contributors guide. Also updated the documentation version.

Merge branch 'master' into tests-fixes-and-contributor-docs

e2a4821

Update README.rst

c1a46c0

Screwed up the documentation links :(

Conengmo merged commit 87bad05 into python-visualization:master Sep 28, 2018

Demetrio92 deleted the tests-fixes-and-contributor-docs branch September 28, 2018 16:44

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Tests fixes and contributor docs #952

Tests fixes and contributor docs #952

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Tests fixes and contributor docs #952

Tests fixes and contributor docs #952

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