datashader
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20 hours ago •
holoviz
holoviz
Trouble running tests with provided conda env
I'm having trouble running the tests locally using the provided conda environment. The environment was created following the instructions in the readme:
conda env create --name datashader --file ./examples/environment.yml
conda activate datashader
pip install -e .
pytest
pytest immediately fails with the following traceback:
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/_pytest/main.py", line 206, in wrap_session
INTERNALERROR> config._do_configure()
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/_pytest/config/__init__.py", line 639, in _do_configure
INTERNALERROR> self.hook.pytest_configure.call_historic(kwargs=dict(config=self))
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/hooks.py", line 311, in call_historic
INTERNALERROR> res = self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/manager.py", line 68, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/manager.py", line 62, in <lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/callers.py", line 208, in _multicall
INTERNALERROR> return outcome.get_result()
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pluggy/callers.py", line 187, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pytest_benchmark/plugin.py", line 1092, in pytest_configure
INTERNALERROR> config._benchmarksession = BenchmarkSession(config)
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pytest_benchmark/plugin.py", line 568, in __init__
INTERNALERROR> self.logger = Logger(self.verbose, config)
INTERNALERROR> File "/Users/isaac/miniconda3/envs/datashader/lib/python3.6/site-packages/pytest_benchmark/plugin.py", line 519, in __init__
INTERNALERROR> self.pytest_warn = config.warn
INTERNALERROR> AttributeError: 'Config' object has no attribute 'warn'
I was able to get tests partially running under a different environment which doesn't have pytest-benchmark installed.
This is using the latest master (3171d8869f63214cc161da755e88c30abe8b5098) with macOS v10.14.3.
Output of `conda list`
# packages in environment at /Users/isaac/miniconda3/envs/datashader:
#
# Name Version Build Channel
affine 2.2.2 py_0 conda-forge
antlr-python-runtime 4.7.2 py36_1000 conda-forge
appnope 0.1.0 py36_1000 conda-forge
asn1crypto 0.24.0 py36_1003 conda-forge
atomicwrites 1.3.0 py_0 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beautifulsoup4 4.7.1 py36_1001 conda-forge
blas 1.1 openblas conda-forge
bleach 3.1.0 py_0 conda-forge
blosc 1.16.3 h0a44026_0 conda-forge
bokeh 1.0.4 py36_1000 conda-forge
boost-cpp 1.68.0 h6f8c590_1000 conda-forge
bzip2 1.0.6 h1de35cc_1002 conda-forge
ca-certificates 2019.3.9 hecc5488_0 conda-forge
cachey 0.1.1 pypi_0 pypi
cairo 1.16.0 h9247486_1000 conda-forge
cartopy 0.17.0 py36h929c6f0_1004 conda-forge
certifi 2019.3.9 py36_0 conda-forge
cf-units 2.1.1 py36h917ab60_1000 conda-forge
cffi 1.12.2 py36h2d6ddff_1 conda-forge
cftime 1.0.3.4 py36h917ab60_1000 conda-forge
chardet 3.0.4 py36_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.0.4 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 0.8.0 py_0 conda-forge
colorcet 1.0.0 py_0 conda-forge
cryptography 2.5 py36hdbc3d79_1 conda-forge
curl 7.64.0 heae2a1f_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cytoolz 0.9.0.1 py36h1de35cc_1001 conda-forge
dask 1.1.4 py_0 conda-forge
dask-core 1.1.4 py_0 conda-forge
datashader 0.7.0a1.post4+g3171d88 dev_0 <develop>
datashape 0.5.4 py_1 conda-forge
decorator 4.3.2 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
descartes 1.1.0 py_2 conda-forge
dill 0.2.9 py36_0 conda-forge
distributed 1.26.0 py36_1 conda-forge
entrypoints 0.3 py36_1000 conda-forge
expat 2.2.5 h0a44026_1002 conda-forge
fastparquet 0.2.1 py36h917ab60_1001 conda-forge
fiona 1.8.4 py36h0e3174d_1002 conda-forge
flake8 3.7.7 py36_0 conda-forge
fontconfig 2.13.1 h1e4e890_1000 conda-forge
freetype 2.9.1 h597ad8a_1005 conda-forge
freexl 1.0.5 h1de35cc_1002 conda-forge
gdal 2.4.0 py36h0e3174d_1002 conda-forge
geopandas 0.4.1 py_0 conda-forge
geos 3.7.1 h0a44026_1000 conda-forge
geotiff 1.4.3 hce09ea4_1000 conda-forge
geoviews 1.6.2 py_0 conda-forge
geoviews-core 1.6.2 py_0 conda-forge
gettext 0.19.8.1 hcca000d_1001 conda-forge
giflib 5.1.4 h1de35cc_1001 conda-forge
glib 2.58.3 h2836805_1001 conda-forge
graphviz 2.38.0 hc6cc99f_1011 conda-forge
hdf4 4.2.13 hf3c6af0_1002 conda-forge
hdf5 1.10.4 nompi_h646315f_1105 conda-forge
heapdict 1.0.0 py36_1000 conda-forge
holoviews 1.11.3 py_0 pyviz/label/dev
icu 58.2 h0a44026_1000 conda-forge
idna 2.8 py36_1000 conda-forge
imageio 2.4.1 py36_1000 conda-forge
ipykernel 5.1.0 py36h24bf2e0_1002 conda-forge
ipython 7.1.1 py36h24bf2e0_1000 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
iris 2.2.0 py36_1003 conda-forge
jedi 0.13.3 py36_0 conda-forge
jinja2 2.10 py_1 conda-forge
jpeg 9c h1de35cc_1001 conda-forge
json-c 0.13.1 h1de35cc_1001 conda-forge
jsonschema 3.0.1 py36_0 conda-forge
jupyter 1.0.0 py_1 conda-forge
jupyter_client 5.2.4 py_3 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
jupyter_dashboards 0.7.0 py36_1000 conda-forge
kealib 1.4.10 hf5ed860_1002 conda-forge
kiwisolver 1.0.1 py36h04f5b5a_1002 conda-forge
krb5 1.16.3 h24a3359_1000 conda-forge
libcurl 7.64.0 h76de61e_0 conda-forge
libcxx 7.0.0 h2d50403_1 conda-forge
libdap4 3.19.1 hae55d67_1000 conda-forge
libedit 3.1.20170329 hcfe32e1_1001 conda-forge
libffi 3.2.1 h0a44026_1005 conda-forge
libgdal 2.4.0 h89caebc_1002 conda-forge
libgfortran 3.0.1 0 conda-forge
libiconv 1.15 h1de35cc_1004 conda-forge
libkml 1.3.0 h71ee1b2_1009 conda-forge
libnetcdf 4.6.2 h6b88ef6_1001 conda-forge
libpng 1.6.36 ha441bb4_1000 conda-forge
libpq 10.6 hbe1e24e_1000 conda-forge
libsodium 1.0.16 h1de35cc_1001 conda-forge
libspatialindex 1.8.5 h0a44026_1003 conda-forge
libspatialite 4.3.0a h0cd9627_1026 conda-forge
libssh2 1.8.0 hf30b1f0_1003 conda-forge
libtiff 4.0.10 h79f4b77_1001 conda-forge
libxml2 2.9.8 hf14e9c8_1005 conda-forge
libxslt 1.1.32 h33a18ac_1002 conda-forge
llvm-meta 7.0.0 0 conda-forge
llvmlite 0.26.0 py36h3fea490_1000 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.3.2 py36h7166777_0 conda-forge
mapclassify 2.0.1 py_0 conda-forge
markupsafe 1.1.1 py36h1de35cc_0 conda-forge
marshmallow 2.19.0 pypi_0 pypi
matplotlib 3.0.3 py36_0 conda-forge
matplotlib-base 3.0.3 py36hf043ca5_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
mistune 0.8.4 py36h1de35cc_1000 conda-forge
more-itertools 4.3.0 py36_1000 conda-forge
msgpack-python 0.6.1 py36h04f5b5a_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.4.1 py_2 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 h0a44026_1002 conda-forge
netcdf4 1.4.3.2 py36hf8bc7f3_0 conda-forge
networkx 2.2 py_1 conda-forge
notebook 5.7.5 py36_0 conda-forge
numba 0.41.0 py36h1702cab_1000 conda-forge
numexpr 2.6.9 py36h1702cab_1000 conda-forge
numpy 1.16.2 py36_blas_openblash486cb9f_0 [blas_openblas] conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.3 hdc02c5d_1001 conda-forge
openjpeg 2.3.0 h3bf0609_1003 conda-forge
openssl 1.0.2r h1de35cc_0 conda-forge
owslib 0.17.1 py_0 conda-forge
packaging 19.0 py_0 conda-forge
pandas 0.24.1 py36h0a44026_0 conda-forge
pandoc 2.6 1 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.8.2 py_0 conda-forge
paramnb 2.0.4 py_0 conda-forge
parso 0.3.4 py_0 conda-forge
partd 0.3.9 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.41 h0a44026_1003 conda-forge
pexpect 4.6.0 py36_1000 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pillow 5.4.1 py36hbddbef0_1000 conda-forge
pip 19.0.3 py36_0 conda-forge
pixman 0.34.0 h1de35cc_1003 conda-forge
pluggy 0.9.0 py_0 conda-forge
poppler 0.67.0 hb974355_6 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 10.6 ha1bbaa7_1000 conda-forge
proj4 5.2.0 h1de35cc_1001 conda-forge
prometheus_client 0.6.0 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
psutil 5.6.0 py36h1de35cc_0 conda-forge
ptyprocess 0.6.0 py36_1000 conda-forge
py 1.8.0 py_0 conda-forge
pycodestyle 2.5.0 py_0 conda-forge
pycparser 2.19 py_0 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pyflakes 2.1.1 py_0 conda-forge
pygments 2.3.1 py_0 conda-forge
pykdtree 1.3.1 py36h917ab60_1002 conda-forge
pyke 1.1.1 py36_1000 conda-forge
pyopenssl 19.0.0 py36_0 conda-forge
pyparsing 2.3.1 py_0 conda-forge
pyproj 1.9.6 py36h9c430a6_1000 conda-forge
pyqt 5.6.0 py36hc26a216_1008 conda-forge
pyrsistent 0.14.11 py36h1de35cc_0 conda-forge
pyshp 2.1.0 py_0 conda-forge
pysocks 1.6.8 py36_1002 conda-forge
pytables 3.4.4 py36h0af8b44_1004 conda-forge
pytest 4.3.0 py36_0 conda-forge
pytest-benchmark 3.0.0 py36_1001 conda-forge
python 3.6.7 h4a56312_1002 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-graphviz 0.10.1 py_0 conda-forge
python-snappy 0.5.3 py36h8522eec_1000 conda-forge
pytz 2018.9 py_0 conda-forge
pyviz_comms 0.7.0 py_0 conda-forge
pywavelets 1.0.2 py36h917ab60_0 conda-forge
pyyaml 3.13 py36h1de35cc_1001 conda-forge
pyzmq 18.0.1 py36h4cc6ddd_0 conda-forge
qt 5.6.2 h822fa55_1013 conda-forge
qtconsole 4.4.3 py_0 conda-forge
rasterio 1.0.21 py36h3683dd5_0 conda-forge
readline 7.0 hcfe32e1_1001 conda-forge
requests 2.21.0 py36_1000 conda-forge
rtree 0.8.3 py36_1000 conda-forge
scikit-image 0.14.2 py36h0a44026_1 conda-forge
scipy 1.2.1 py36_blas_openblash486cb9f_0 [blas_openblas] conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 40.8.0 py36_0 conda-forge
shapely 1.6.4 py36h2bcc7ef_1002 conda-forge
sip 4.18.1 py36h0a44026_1000 conda-forge
six 1.12.0 py36_1000 conda-forge
snappy 1.1.7 h0a44026_1002 conda-forge
snuggs 1.4.3 py_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
soupsieve 1.8 py36_0 conda-forge
sqlite 3.26.0 h1765d9f_1001 conda-forge
statsmodels 0.9.0 py36h917ab60_1000 conda-forge
streamz 0.2.0 pypi_0 pypi
tblib 1.3.2 py_1 conda-forge
terminado 0.8.1 py36_1001 conda-forge
testpath 0.3.1 pypi_0 pypi
thrift 0.11.0 py36h0a44026_1001 conda-forge
tk 8.6.9 ha441bb4_1000 conda-forge
toolz 0.9.0 py_1 conda-forge
tornado 6.0.1 py36h1de35cc_0 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
tzcode 2018g h1de35cc_1001 conda-forge
udunits2 2.2.27.6 h776b7f1_1001 conda-forge
urllib3 1.24.1 py36_1000 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webargs 5.1.2 pypi_0 pypi
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.1 py36_0 conda-forge
widgetsnbextension 3.4.2 py36_1000 conda-forge
xarray 0.11.3 py36_0 conda-forge
xerces-c 3.2.2 h44e365a_1001 conda-forge
xz 5.2.4 h1de35cc_1001 conda-forge
yaml 0.1.7 h1de35cc_1001 conda-forge
zeromq 4.2.5 h0a44026_1006 conda-forge
zict 0.1.4 py_0 conda-forge
zlib 1.2.11 h1de35cc_1004 conda-forge
Thanks for any help!
I think examples/environment.yml is probably out of date - the dependencies are quite different from the current ones (see https://github.com/pyviz/datashader/blob/master/setup.py#L32, which is the basis for the conda package).
In the short term, maybe you could conda install -c pyviz datashader and then remove --force it (to leave the dependencies), then do pip install -e . --no-deps in the git repo? I have not tested this, and a current datashader developer might have a better idea. Or maybe you could look to see what pins there are in setup.py (e.g. see the pytest and pytest-benchmark pins...), and apply them to your existing environment?
The plan for datashader was to specify the dependencies in one place, and generate both the conda package recipe and examples/environment.yml from that (by filtering/pinning/combining groups as necessary for each one, since they have different purposes). I think we've managed to start doing that in some other pyviz projects (e.g. pyviz itself), but we're not there yet.
Sounds about right. I think @jsignell can fix environment.yml to be generated from the actual dependencies, so that it matches what we use for testing. But I don't think any removing is needed; I just do conda install -c pyviz datashader then pip install -e . inside the datashader repo, which is normally sufficient to ensure that the repo is used rather than the conda package.
Thanks for the advice!
I'm still having trouble though. Here's what I've run so far:
conda create -n datashader
conda activate datashader
conda install --deps-only -yc pyviz datashader
At this point, pytest isn't in the environment, so I've manually added the test requirements from the setup.py:
conda install -y "pytest==3.9.3" "pytest-benchmark==3.0.0" "flake8" "nbsmoke>=0.2.6" "fastparquet>=0.1.6"
pip install -e .
Running pytest at this point throws a tornado error:
Call & traceback
(datashader) isaac@mimir ~/github/datashader$ pytest ✭speedup_connectedges
Traceback (most recent call last):
File "/Users/isaac/miniconda3/envs/datashader/bin/pytest", line 11, in <module>
sys.exit(main())
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/config/__init__.py", line 56, in main
config = _prepareconfig(args, plugins)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/config/__init__.py", line 193, in _prepareconfig
pluginmanager=pluginmanager, args=args
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/hooks.py", line 289, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/manager.py", line 68, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/manager.py", line 62, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall
gen.send(outcome)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/helpconfig.py", line 93, in pytest_cmdline_parse
config = outcome.get_result()
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
raise ex[1].with_traceback(ex[2])
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/config/__init__.py", line 663, in pytest_cmdline_parse
self.parse(args)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/config/__init__.py", line 835, in parse
self._preparse(args, addopts=addopts)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/_pytest/config/__init__.py", line 787, in _preparse
self.pluginmanager.load_setuptools_entrypoints("pytest11")
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pluggy/manager.py", line 274, in load_setuptools_entrypoints
plugin = ep.load()
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2411, in load
return self.resolve()
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2417, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/nbsmoke/__init__.py", line 94, in <module>
import nbconvert
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/nbconvert/__init__.py", line 7, in <module>
from . import postprocessors
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/nbconvert/postprocessors/__init__.py", line 5, in <module>
from .serve import ServePostProcessor
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/nbconvert/postprocessors/serve.py", line 19, in <module>
class ProxyHandler(web.RequestHandler):
File "/Users/isaac/miniconda3/envs/datashader/lib/python3.7/site-packages/nbconvert/postprocessors/serve.py", line 21, in ProxyHandler
@web.asynchronous
AttributeError: module 'tornado.web' has no attribute 'asynchronous'
Output of `conda list`
# packages in environment at /Users/isaac/miniconda3/envs/datashader:
#
# Name Version Build Channel
appnope 0.1.0 py37_0
asn1crypto 0.24.0 py37_0
atomicwrites 1.3.0 py_0
attrs 19.1.0 py_0
backcall 0.1.0 py37_0
beautifulsoup4 4.7.1 py37_1
blas 1.0 mkl
bleach 3.1.0 py37_0
bokeh 1.0.4 py37_0
ca-certificates 2019.1.23 0
certifi 2019.3.9 py37_0
cffi 1.12.2 py37hb5b8e2f_1
chardet 3.0.4 py37_1
click 7.0 py37_0
cloudpickle 0.8.0 py37_0
colorcet 1.0.1 py_0 pyviz
cryptography 2.6.1 py37ha12b0ac_0
cycler 0.10.0 py37_0
cytoolz 0.9.0.1 py37h1de35cc_1
dask 1.1.4 py_0
dask-core 1.1.4 py_0
datashader 0.7.0a1.post5+g7fa33cb dev_0 <develop>
datashape 0.5.4 py37_1
decorator 4.3.2 py37_0
distributed 1.26.0 py37_1
entrypoints 0.3 py37_0
fastparquet 0.2.1 py37h1d22016_1
flake8 3.7.7 py37_0
freetype 2.9.1 hb4e5f40_0
heapdict 1.0.0 py37_2
idna 2.8 py37_0
imageio 2.5.0 py37_0
intel-openmp 2019.1 144
ipykernel 5.1.0 py37h39e3cac_0
ipython 7.3.0 py37h39e3cac_0
ipython_genutils 0.2.0 py37_0
jedi 0.13.3 py37_0
jinja2 2.10 py37_0
jpeg 9b he5867d9_2
jsonschema 3.0.1 py37_0
jupyter_client 5.2.4 py37_0
jupyter_core 4.4.0 py37_0
kiwisolver 1.0.1 py37h0a44026_0
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 h475c297_4
libgfortran 3.0.1 h93005f0_2
libpng 1.6.36 ha441bb4_0
libsodium 1.0.16 h3efe00b_0
libtiff 4.0.10 hcb84e12_2
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nbsmoke 0.2.7 py_0 conda-forge
ncurses 6.1 h0a44026_1
networkx 2.2 py37_1
numba 0.42.0 py37h6440ff4_0
numpy 1.16.2 py37hacdab7b_0
numpy-base 1.16.2 py37h6575580_0
olefile 0.46 py37_0
openssl 1.1.1b h1de35cc_1
packaging 19.0 py37_0
pandas 0.24.1 py37h0a44026_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py37_1
param 1.8.2 py_0 pyviz
parso 0.3.4 py37_0
partd 0.3.9 py37_0
pexpect 4.6.0 py37_0
pickleshare 0.7.5 py37_0
pillow 5.4.1 py37hb68e598_0
pip 19.0.3 py37_0
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py 1.8.0 py37_0
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pygments 2.3.1 py37_0
pyopenssl 19.0.0 py37_0
pyparsing 2.3.1 py37_0
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pytest 3.9.3 py37_0
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python 3.7.2 haf84260_0
python-dateutil 2.8.0 py37_0
pytz 2018.9 py37_0
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Progress! I got rid of the tornado error by downgrading tornado. Now pytest runs, but for some reason it's not finding all the tests. Here's the full set of commands to get to my current environment:
conda create -n datashader
conda activate datashader
conda install --deps-only -yc pyviz datashader
conda install -y "pytest==3.9.3" "pytest-benchmark==3.0.0" "flake8" "nbsmoke>=0.2.6" "fastparquet>=0.1.6"
conda install "tornado<=6"
pip install -e .
However, not all the tests are running. I think a similar issue is happening with the travis builds. In the build for my PR (#725) I noticed travis was passing while appveyor wasn't. Neither should pass, since there are two test which are failing, since I think those tests have a bug. Travis just isn't running those tests (travis logs don't show tests from test_bundling.py).
Looking into this a little further, pytest --collect-only . collects 425 tests (skipping 12) from the conda environment, but using a pip installed pytest (v4.3.0) 461 items are collected with 5 skipped.
Running pytest --collect-only --disable-warnings . | pbcopy I find:
conda env collected tests
============================= test session starts ==============================
platform darwin -- Python 3.7.2, pytest-3.9.3, py-1.8.0, pluggy-0.9.0 -- /Users/isaac/miniconda3/envs/datashader/bin/python
cachedir: .pytest_cache
benchmark: 3.0.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=5.00us max_time=1.00s calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/isaac/github/datashader, inifile: tox.ini
plugins: benchmark-3.0.0, nbsmoke-0.2.7
collecting ... collected 425 items / 12 skipped
<Package '/Users/isaac/github/datashader/datashader'>
<DoctestModule 'colors.py'>
<DoctestItem 'datashader.colors.colormap_select'>
<DoctestItem 'datashader.colors.hex_to_rgb'>
<DoctestItem 'datashader.colors.rgb'>
<DoctestModule 'core.py'>
<DoctestItem 'datashader.core.Axis'>
<DoctestItem 'datashader.core.Canvas.line'>
<DoctestItem 'datashader.core.Canvas.trimesh'>
<DoctestModule 'reductions.py'>
<DoctestItem 'datashader.reductions.summary'>
<DoctestModule 'utils.py'>
<DoctestItem 'datashader.utils.isreal'>
<Package '/Users/isaac/github/datashader/datashader/spatial'>
<DoctestModule 'points.py'>
<DoctestItem 'datashader.spatial.points.SpatialPointsFrame'>
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<Function 'test_shade[span1-a]'>
<Function 'test_shade[span1-b]'>
<Function 'test_shade[span1-c]'>
<Function 'test_shade[span2-a]'>
<Function 'test_shade[span2-b]'>
<Function 'test_shade[span2-c]'>
<Function 'test_span_cmap_list[linear-a]'>
<Function 'test_span_cmap_list[linear-b]'>
<Function 'test_span_cmap_list[linear-c]'>
<Function 'test_span_cmap_list[log-a]'>
<Function 'test_span_cmap_list[log-b]'>
<Function 'test_span_cmap_list[log-c]'>
<Function 'test_span_cmap_list[cbrt-a]'>
<Function 'test_span_cmap_list[cbrt-b]'>
<Function 'test_span_cmap_list[cbrt-c]'>
<Function 'test_span_cmap_single[black]'>
<Function 'test_span_cmap_single[cmap1]'>
<Function 'test_span_cmap_single[#000000]'>
<Function 'test_span_cmap_mpl'>
<Function 'test_shade_bool'>
<Function 'test_shade_cmap'>
<Function 'test_shade_cmap_non_categorical_alpha[black]'>
<Function 'test_shade_cmap_non_categorical_alpha[cmap1]'>
<Function 'test_shade_cmap_non_categorical_alpha[#000000]'>
<Function 'test_shade_cmap_errors'>
<Function 'test_shade_mpl_cmap'>
<Function 'test_shade_category'>
<Function 'test_set_background'>
<Function 'test_stack'>
<Function 'test_masks'>
<Function 'test_spread'>
<Function 'test_density'>
<Function 'test_dynspread'>
<Function 'test_eq_hist'>
<Function 'test_Image_to_pil'>
<Function 'test_Image_to_bytesio'>
<Function 'test_shade_should_handle_zeros_array'>
<Module 'test_utils.py'>
<Function 'test_Dispatcher'>
<Function 'test_isreal'>
<Module 'test_xarray.py'>
<Function 'test_count[source0]'>
<Function 'test_count[source1]'>
<Function 'test_count[source2]'>
<Function 'test_count[source3]'>
<Module 'test_canvas.py'>
<Function 'test_line'>
<Function 'test_points'>
<Module 'test_draw_line.py'>
<Function 'test_draw_line_left_border'>
<Function 'test_draw_line_diagonal'>
<Function 'test_draw_line_offset'>
<Module 'test_extend_line.py'>
<Function 'test_extend_line_uniform[0-0]'>
<Function 'test_extend_line_uniform[0-100000]'>
<Function 'test_extend_line_uniform[-100000-0]'>
<Function 'test_extend_line_uniform[-100000-100000]'>
<Function 'test_extend_line_normal'>
<Module 'test_layout.py'>
<Function 'test_layout[random_layout]'>
<Function 'test_layout[circular_layout]'>
<Function 'test_layout[forceatlas2_layout]'>
=================== 12 skipped, 14 warnings in 5.56 seconds ====================
pytest 4.3.0 collected tests
============================= test session starts ==============================
platform darwin -- Python 3.7.2, pytest-4.3.0, py-1.8.0, pluggy-0.8.1 -- /usr/local/opt/python/bin/python3.7
cachedir: .pytest_cache
rootdir: /Users/isaac/github/datashader, inifile: tox.ini
plugins: xdist-1.26.0, parallel-0.0.9, mock-1.10.1, helpers-namespace-2019.1.8, forked-1.0.1, cov-2.6.1, pylama-7.6.6
collecting ... collected 461 items / 5 skipped / 456 selected
<Package /Users/isaac/github/datashader/datashader>
<DoctestModule colors.py>
<DoctestItem datashader.colors.colormap_select>
<DoctestItem datashader.colors.hex_to_rgb>
<DoctestItem datashader.colors.rgb>
<DoctestModule core.py>
<DoctestItem datashader.core.Axis>
<DoctestItem datashader.core.Canvas.line>
<DoctestItem datashader.core.Canvas.trimesh>
<DoctestModule reductions.py>
<DoctestItem datashader.reductions.summary>
<DoctestModule utils.py>
<DoctestItem datashader.utils.isreal>
<Package /Users/isaac/github/datashader/datashader/spatial>
<DoctestModule points.py>
<DoctestItem datashader.spatial.points.SpatialPointsFrame>
<Package /Users/isaac/github/datashader/datashader/tests>
<Module test_bokeh_ext.py>
<Function test_interactive_image_initialize>
<Function test_interactive_image_update>
<Module test_bundling.py>
<Function test_immutable_nodes>
<Function test_renamed_columns[connect_edges]>
<Function test_renamed_columns[hammer_bundle]>
<Function test_same_path_endpoints[random_layout-connect_edges]>
<Function test_same_path_endpoints[random_layout-hammer_bundle]>
<Function test_same_path_endpoints[circular_layout-connect_edges]>
<Function test_same_path_endpoints[circular_layout-hammer_bundle]>
<Function test_same_path_endpoints[forceatlas2_layout-connect_edges]>
<Function test_same_path_endpoints[forceatlas2_layout-hammer_bundle]>
<Function test_directly_connect_with_weights[True]>
<Function test_directly_connect_with_weights[False]>
<Function test_directly_connect_without_weights[True]>
<Function test_directly_connect_without_weights[False]>
<Function test_hammer_bundle_with_weights[True]>
<Function test_hammer_bundle_with_weights[False]>
<Function test_hammer_bundle_without_weights[True]>
<Function test_hammer_bundle_without_weights[False]>
<Module test_colors.py>
<Function test_hex_to_rgb>
<Function test_rgb>
<Module test_compatibility.py>
<Function test__exec>
<Function test_apply>
<Module test_composite.py>
<Function test_source>
<Function test_over>
<Function test_add>
<Function test_saturate>
<Module test_dask.py>
<Function test_count>
<Function test_any>
<Function test_sum>
<Function test_min>
<Function test_max>
<Function test_mean>
<Function test_var>
<Function test_std>
<Function test_count_cat>
<Function test_multiple_aggregates>
<Function test_auto_range_points>
<Function test_uniform_points>
<Function test_uniform_diagonal_points[0-9]>
<Function test_uniform_diagonal_points[0-10]>
<Function test_uniform_diagonal_points[0-99]>
<Function test_uniform_diagonal_points[0-100]>
<Function test_log_axis_points>
<Function test_line>
<Function test_line_manual_range[df0-x0-y0-1]>
<Function test_line_manual_range[df1-x1-y1-1]>
<Function test_line_manual_range[df2-x-y-0]>
<Function test_line_manual_range[df3-x3-y3-0]>
<Function test_line_manual_range[df4-x0-y4-0]>
<Function test_line_manual_range[df5-x-y-1]>
<Function test_line_autorange[df0-x0-y0-1]>
<Function test_line_autorange[df1-x1-y1-1]>
<Function test_line_autorange[df2-x-y-0]>
<Function test_line_autorange[df3-x3-y3-0]>
<Function test_line_autorange[df4-x4-y0-0]>
<Function test_line_autorange[df5-x-y-1]>
<Function test_line_x_constant_autorange>
<Function test_log_axis_line>
<Function test_auto_range_line>
<Function test_trimesh_no_double_edge>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_dask_partitions[1]>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_dask_partitions[2]>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_dask_partitions[3]>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_dask_partitions[4]>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_dask_partitions[5]>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Module test_datatypes.py>
<Function test_construct_ragged_dtype>
<Function test_construct_ragged_array>
<Function test_construct_ragged_array_from_ragged_array>
<Function test_construct_ragged_array_fastpath>
<Function test_validate_ragged_array_fastpath>
<Function test_start_indices_dtype>
<Function test_flat_array_type_inference[arg0-int64]>
<Function test_flat_array_type_inference[arg1-bool]>
<Function test_flat_array_type_inference[arg2-int32]>
<Function test_flat_array_type_inference[arg3-float64]>
<Function test_flat_array_type_inference[arg4-float32]>
<Function test_isna>
<Function test_get_item_scalar>
<Function test_get_item_scalar_out_of_bounds[-1000]>
<Function test_get_item_scalar_out_of_bounds[-6]>
<Function test_get_item_scalar_out_of_bounds[5]>
<Function test_get_item_scalar_out_of_bounds[1000]>
<Function test_get_item_slice>
<Function test_get_item_mask[mask0]>
<Function test_get_item_mask[mask1]>
<Function test_get_item_mask[mask2]>
<Function test_get_item_list[inds0]>
<Function test_get_item_list[inds1]>
<Function test_get_item_list[inds2]>
<Function test_get_item_list[inds3]>
<Function test_get_item_list[inds4]>
<Function test_factorization>
<Function test_from_sequence>
<Function test_copy>
<Function test_take>
<Function test_concat_same_type>
<Function test_pandas_array_construction>
<Function test_series_construction>
<Function test_concat_series>
<Function test_array_eq_scalar[scalar0]>
<Function test_array_eq_scalar[scalar1]>
<Function test_array_eq_numpy1>
<Function test_array_eq_numpy2d>
<Function test_array_eq_ragged>
<Function test_equality_validation[a string]>
<Function test_equality_validation[32]>
<Function test_equality_validation[other2]>
<Function test_equality_validation[other3]>
<Function test_equality_validation[other4]>
<Class TestRaggedConstructors>
<Function test_from_sequence_from_cls>
<Function test_array_from_scalars>
<Function test_series_constructor>
<Function test_dataframe_constructor_from_dict[True]>
<Function test_dataframe_constructor_from_dict[False]>
<Function test_dataframe_from_series>
<Function test_series_given_mismatched_index_raises>
<Function test_from_dtype>
<Function test_pandas_array>
<Function test_pandas_array_dtype>
<Class TestRaggedDtype>
<Function test_name>
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<Function test_is_dtype_from_self>
<Function test_is_not_string_type>
<Function test_is_not_object_type>
<Function test_eq_with_str>
<Function test_eq_with_numpy_object>
<Function test_eq_with_self>
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<Class TestRaggedGetitem>
<Function test_get>
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<Function test_take>
<Function test_iloc_series>
<Function test_iloc_frame>
<Function test_loc_series>
<Function test_loc_frame>
<Function test_getitem_scalar>
<Function test_getitem_scalar_na>
<Function test_getitem_mask>
<Function test_getitem_slice>
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<Function test_take_non_na_fill_value>
<Function test_take_pandas_style_negative_raises>
<Function test_take_out_of_bounds_raises[True]>
<Function test_take_out_of_bounds_raises[False]>
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<Function test_groupby_extension_apply[object]>
<Function test_grouping_grouper>
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<Class TestRaggedInterface>
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<Function test_can_hold_na_valid>
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<Function test_is_numeric_honored>
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<Class TestRaggedMethods>
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<Function test_unique[<lambda>-Series]>
<Function test_unique[<lambda>-<lambda>]>
<Function test_unique[unique-Series]>
<Function test_unique[unique-<lambda>]>
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<Function test_fillna_copy_series>
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<Function test_combine_add>
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<Function test_count>
<Function test_apply_simple_series>
<Function test_argsort>
<Function test_argsort_missing>
<Function test_sort_values[True]>
<Function test_sort_values[False]>
<Function test_sort_values_missing[True]>
<Function test_sort_values_missing[False]>
<Function test_sort_values_frame[True]>
<Function test_sort_values_frame[False]>
<Function test_factorize[-1]>
<Function test_factorize[-2]>
<Function test_factorize_equivalence[-1]>
<Function test_factorize_equivalence[-2]>
<Function test_factorize_empty>
<Function test_fillna_length_mismatch>
<Function test_container_shift[-2-indices0-True]>
<Function test_container_shift[-2-indices0-False]>
<Function test_container_shift[0-indices1-True]>
<Function test_container_shift[0-indices1-False]>
<Function test_container_shift[2-indices2-True]>
<Function test_container_shift[2-indices2-False]>
<Function test_shift_non_empty_array[-4-indices0]>
<Function test_shift_non_empty_array[-1-indices1]>
<Function test_shift_non_empty_array[0-indices2]>
<Function test_shift_non_empty_array[1-indices3]>
<Function test_shift_non_empty_array[4-indices4]>
<Function test_shift_empty_array[-4]>
<Function test_shift_empty_array[-1]>
<Function test_shift_empty_array[0]>
<Function test_shift_empty_array[1]>
<Function test_shift_empty_array[4]>
<Function test_shift_fill_value>
<Function test_hash_pandas_object_works[True]>
<Function test_hash_pandas_object_works[False]>
<Function test_searchsorted[True]>
<Function test_searchsorted[False]>
<Function test_where_series[True]>
<Function test_where_series[False]>
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<Function test_repeat[0-False-False]>
<Function test_repeat[1-True-True]>
<Function test_repeat[1-True-False]>
<Function test_repeat[1-False-True]>
<Function test_repeat[1-False-False]>
<Function test_repeat[2-True-True]>
<Function test_repeat[2-True-False]>
<Function test_repeat[2-False-True]>
<Function test_repeat[2-False-False]>
<Function test_repeat[repeats3-True-True]>
<Function test_repeat[repeats3-True-False]>
<Function test_repeat[repeats3-False-True]>
<Function test_repeat[repeats3-False-False]>
<Function test_repeat_raises[2-kwargs0-ValueError-'axis-True]>
<Function test_repeat_raises[2-kwargs0-ValueError-'axis-False]>
<Function test_repeat_raises[-1-kwargs1-ValueError-negative-True]>
<Function test_repeat_raises[-1-kwargs1-ValueError-negative-False]>
<Function test_repeat_raises[repeats2-kwargs2-ValueError-shape-True]>
<Function test_repeat_raises[repeats2-kwargs2-ValueError-shape-False]>
<Function test_repeat_raises[2-kwargs3-TypeError-'foo'-True]>
<Function test_repeat_raises[2-kwargs3-TypeError-'foo'-False]>
<Class TestRaggedPrinting>
<Function test_array_repr[big]>
<Function test_array_repr[small]>
<Function test_array_repr_unicode>
<Function test_series_repr>
<Function test_dataframe_repr>
<Function test_dtype_name_in_info>
<Class TestRaggedMissing>
<Function test_fillna_series>
<Function test_fillna_frame>
<Function test_isna>
<Function test_dropna_array>
<Function test_dropna_series>
<Function test_dropna_frame>
<Function test_fillna_scalar>
<Function test_fillna_limit_pad>
<Function test_fillna_limit_backfill>
<Function test_fillna_series_method[ffill]>
<Function test_fillna_series_method[bfill]>
<Function test_fillna_fill_other>
<Class TestRaggedReshaping>
<Function test_concat[True]>
<Function test_concat[False]>
<Function test_concat_all_na_block[True]>
<Function test_concat_all_na_block[False]>
<Function test_concat_mixed_dtypes>
<Function test_concat_columns>
<Function test_align>
<Function test_align_frame>
<Function test_align_series_frame>
<Function test_set_frame_expand_regular_with_extension>
<Function test_set_frame_expand_extension_with_regular>
<Function test_set_frame_overwrite_object>
<Function test_merge>
<Function test_merge_on_extension_array>
<Function test_merge_on_extension_array_duplicates>
<Function test_stack[columns0]>
<Function test_stack[columns1]>
<Function test_unstack[series-index0]>
<Function test_unstack[series-index1]>
<Function test_unstack[series-index2]>
<Function test_unstack[series-index3]>
<Function test_unstack[frame-index0]>
<Function test_unstack[frame-index1]>
<Function test_unstack[frame-index2]>
<Function test_unstack[frame-index3]>
<Module test_geo.py>
<Function test_mean_transfer_function>
<Function test_slope_transfer_function>
Assert slope transfer function
<Function test_aspect_transfer_function>
Assert aspect transfer function
<Function test_hillshade_simple_transfer_function>
Assert Simple Hillshade transfer function
<Function test_ndvi_transfer_function>
Assert aspect transfer function
<Function test_generate_terrain>
<Function test_bump>
<Module test_glyphs.py>
<Function test_point_bounds_check>
<Function test_point_validate>
<Function test_draw_line>
<Function test_draw_line_same_point>
<Function test_draw_line_vertical_horizontal>
<Function test_extend_lines>
<Function test_extend_lines_all_out_of_bounds>
<Function test_extend_lines_nan>
<Function test_extend_lines_exact_bounds>
<Function test_draw_triangle_nointerp>
Assert that we draw triangles properly, without interpolation enabled.
<Function test_draw_triangle_interp>
Assert that we draw triangles properly, with interpolation enabled.
<Function test_draw_triangle_subpixel>
Assert that we draw subpixel triangles properly, both with and without
interpolation.
<Function test_line_awkward_point_on_upper_bound_maps_to_last_pixel>
Check that point deliberately chosen to be on the upper bound but
with a similar-magnitudes subtraction error like that which could
occur in extend line does indeed get mapped to last pixel.
<Function test_lines_xy_validate>
<Module test_layout.py>
<Function test_renamed_columns[random_layout-connect_edges]>
<Function test_renamed_columns[random_layout-hammer_bundle]>
<Function test_renamed_columns[circular_layout-connect_edges]>
<Function test_renamed_columns[circular_layout-hammer_bundle]>
<Function test_renamed_columns[forceatlas2_layout-connect_edges]>
<Function test_renamed_columns[forceatlas2_layout-hammer_bundle]>
<Function test_forceatlas2_positioned_nodes_with_unweighted_edges>
<Function test_forceatlas2_positioned_nodes_with_weighted_edges>
<Function test_forceatlas2_unpositioned_nodes_with_unweighted_edges>
<Function test_forceatlas2_unpositioned_nodes_with_weighted_edges>
<Function test_random_layout>
<Function test_uniform_circular_layout>
<Function test_random_circular_layout>
<Module test_pandas.py>
<Function test_count>
<Function test_any>
<Function test_sum>
<Function test_min>
<Function test_max>
<Function test_mean>
<Function test_var>
<Function test_std>
<Function test_count_cat>
<Function test_multiple_aggregates>
<Function test_auto_range_points>
<Function test_uniform_points>
<Function test_uniform_diagonal_points[0-9]>
<Function test_uniform_diagonal_points[0-10]>
<Function test_uniform_diagonal_points[0-99]>
<Function test_uniform_diagonal_points[0-100]>
<Function test_log_axis_points>
<Function test_line>
<Function test_points_on_edge>
<Function test_lines_on_edge>
<Function test_log_axis_line>
<Function test_auto_range_line>
<Function test_trimesh_no_double_edge>
Assert that when two triangles share an edge that would normally get
double-drawn, the edge is only drawn for the rightmost (or bottommost)
triangle.
<Function test_trimesh_interp>
Assert that triangles are interpolated when vertex values are provided.
<Function test_trimesh_simplex_weights>
Assert that weighting the simplices works as expected.
<Function test_trimesh_vertex_weights>
Assert that weighting the vertices works as expected.
<Function test_trimesh_winding_detect>
Assert that CCW windings get converted to CW.
<Function test_trimesh_mesharg>
Assert that the ``mesh`` argument results in the same rasterization,
despite the ``vertices`` and ``simplices`` arguments changing.
<Function test_trimesh_agg_api>
Assert that the trimesh aggregation API properly handles weights on the simplices.
<Function test_bug_570>
<Function test_line_manual_range[df0-x0-y0-1]>
<Function test_line_manual_range[df1-x1-y1-1]>
<Function test_line_manual_range[df2-x2-y2-1]>
<Function test_line_manual_range[df3-x-y-0]>
<Function test_line_manual_range[df4-x4-y4-0]>
<Function test_line_manual_range[df5-x5-y0-0]>
<Function test_line_manual_range[df6-x-y-1]>
<Function test_line_autorange[df0-x0-y0-1]>
<Function test_line_autorange[df1-x1-y1-1]>
<Function test_line_autorange[df2-x-y-0]>
<Function test_line_autorange[df3-x3-y3-0]>
<Function test_line_autorange[df4-x4-y0-0]>
<Function test_line_autorange[df5-x-y-1]>
<Function test_line_autorange_axis1_x_constant>
<Function test_line_agg_sum_axis1_none_constant>
<Function test_line_autorange_axis1_ragged>
<Module test_pipeline.py>
<Function test_pipeline>
<Module test_spatial.py>
<Function test_spatial_points_frame_properties[False]>
<Function test_spatial_points_frame_properties[True]>
<Function test_query_partitions[False-x_range0-y_range0]>
<Function test_query_partitions[False-x_range1-y_range1]>
<Function test_query_partitions[False-x_range2-y_range2]>
<Function test_query_partitions[True-x_range0-y_range0]>
<Function test_query_partitions[True-x_range1-y_range1]>
<Function test_query_partitions[True-x_range2-y_range2]>
<Function test_aggregation_partitions[False-x_range0-y_range0]>
<Function test_aggregation_partitions[False-x_range1-y_range1]>
<Function test_aggregation_partitions[False-x_range2-y_range2]>
<Function test_aggregation_partitions[True-x_range0-y_range0]>
<Function test_aggregation_partitions[True-x_range1-y_range1]>
<Function test_aggregation_partitions[True-x_range2-y_range2]>
<Function test_validate_parquet_file>
<Module test_tiles.py>
<Function test_render_tiles>
<Function test_get_super_tile_min_max>
<Function test_calculate_zoom_level_stats_with_fullscan_ranging_strategy>
<Module test_transfer_functions.py>
<Function test_shade[None-a]>
<Function test_shade[None-b]>
<Function test_shade[None-c]>
<Function test_shade[span1-a]>
<Function test_shade[span1-b]>
<Function test_shade[span1-c]>
<Function test_shade[span2-a]>
<Function test_shade[span2-b]>
<Function test_shade[span2-c]>
<Function test_span_cmap_list[linear-a]>
<Function test_span_cmap_list[linear-b]>
<Function test_span_cmap_list[linear-c]>
<Function test_span_cmap_list[log-a]>
<Function test_span_cmap_list[log-b]>
<Function test_span_cmap_list[log-c]>
<Function test_span_cmap_list[cbrt-a]>
<Function test_span_cmap_list[cbrt-b]>
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==================== 5 skipped, 16 warnings in 4.73 seconds ====================
I did:
conda create -n datashader -c pyviz/label/dev datashader
conda activate datashader
pip install -e .[tests]
I was getting 12 skips from having a broken version of skimage:
>>> import skimage
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/jsignell/conda/envs/ds-14/lib/python3.7/site-packages/skimage/__init__.py", line 167, in <module>
from .util.dtype import (img_as_float32,
File "/Users/jsignell/conda/envs/ds-14/lib/python3.7/site-packages/skimage/util/__init__.py", line 8, in <module>
from .arraycrop import crop
File "/Users/jsignell/conda/envs/ds-14/lib/python3.7/site-packages/skimage/util/arraycrop.py", line 8, in <module>
from numpy.lib.arraypad import _validate_lengths
ImportError: cannot import name '_validate_lengths' from 'numpy.lib.arraypad' (/Users/jsignell/conda/envs/ds-14/lib/python3.7/site-packages/numpy/lib/arraypad.py)
I upgraded scikit-image to 0.14.2 from conda-forge (conda install -c conda-forge scikit-image=0.14.2) and got 5 skips. Then I got rasterio and am down to 3 skips in collection - but that's when I saw failures crop up:
datashader/tests/test_raster.py::test_raster_aggregate_default FAILED
datashader/tests/test_raster.py::test_raster_aggregate_nearest FAILED
datashader/tests/test_raster.py::test_partial_extent_returns_correct_size FAILED
datashader/tests/test_raster.py::test_raster_single_pixel_range_with_padding FAILED
Just an aside: I see above in a few places using pip install -e . in conda environments. Maybe that's ok now with the latest conda, or if you know what you're doing, but I always avoided it because it installs any dependencies not already present using pip, which can be confusing and/or problematic in a conda environment. When I used conda, I always did pip install -e . --no-deps. pip install -e . --no-deps into a conda environment is still not perfect, because e.g. things like entry points will then be done by setuptools rather than by conda.
(python setup.py develop may be worse still depending on what you want, because missing dependencies will be installed with easy_install, you won't be using wheels, and so on...)
can be confusing and/or problematic in a conda environment
Right; I always conda-install the released package first, then run pip install --no-deps -e ., which uses conda to install the dependencies then sets up the github master as the actual module in use. Of course, that will go wrong if dependencies are different in master than they are in the latest release, but I don't know of any solution that is any better in that respect.
The examples/environment.yml file is indeed somewhat out of date. Rather than update it, I am inclined to remove it and change the developer install instructions in the README to use pyctdev as we do in our CI. Then the two setup files remain the single source of dependency information for both pip and conda installs. It will be a little confusing for new developers who are not familiar with pyctdev, but if the instructions are followed precisely we can guarantee that the install will work as we use the same workflow in our CI.
Does pyctdev do better than the conda + pip -e solution?
It is not intrinsically any better, but in practice it is better because it uses the setup files to obtain the list of dependencies and they are always up to date. conda install uses the environment.yml file which is not necessary in sync with the setup files because neither developers nor CI use this approach.
Sorry. I didn't mean conda+environment.yml + pip -e, I meant just conda install -c pyviz datashader to get the latest released datashader, followed by pip install --no-deps -e . in the git repo clone. That's what I always do, and it's been reliable so far despite @ceball's fearmongering above. :-) I do think we should delete the outdated environment.yml file, since there's no automatic mechanism to keep it up to date, and I don't want to start a project to make it be auto-generated to be accurate.
It's true that my method won't always install the latest dependencies, if those have been updated in git master but not yet released, but I haven't noticed that to be a problem in practice. We rarely add new dependencies, and when we do they are typically for specific examples, not the core library itself. We can of course tell people to use pyctdev like the CI does to avoid that problem, but my question is whether using pyctdev provides benefits that are worth the extra cognitive load of learning about it. I'm not sure it does, but am open to learning about some benefit it provides for a developer that is worthwhile.
I understand now!
I think your approach is absolutely fine now. My default approach is even simpler, just a pip install -e .[tests,examples] in a clean virtual environment, which is fine on Linux but may be less so on other platforms.
OK, so plan A is to remove the environment.yml file and not mention pyctdev any more than we already do. I'll write a PR to do this and update the README with the preferred dev installation process, but before that I will check exactly what does work on the 3 major platforms.