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Tests failing on Alpine Linux #583

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russkel opened this issue Mar 26, 2020 · 11 comments
Closed

Tests failing on Alpine Linux #583

russkel opened this issue Mar 26, 2020 · 11 comments
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@russkel
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russkel commented Mar 26, 2020 •
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Hi, I am trying to compile the pyproj library on Alpine Linux. I filed a few bug fixes with the proj project (and musl libc) that were all fixed enabling the proj library to compile and pass tests on Alpine Linux 32/64b on a number of architectures. I am not having similar luck with pyproj though.

Problem description

Please see the attached build and test log, there are a number of failures:

job.log

Failures

=================================== FAILURES ===================================
_______________________________ test_datum[Proj] _______________________________

proj_class = <class 'pyproj.proj.Proj'>, aoi_data_directory = None

    @pytest.mark.parametrize("proj_class", [Proj, CRS])
    def test_datum(proj_class, aoi_data_directory):
        p1 = proj_class(proj="latlong", datum="WGS84")
        s_1 = -111.5
        s_2 = 45.25919444444
        p2 = proj_class(proj="utm", zone=10, datum="NAD27")
        x2, y2 = transform(p1, p2, s_1, s_2)
        if LooseVersion(proj_version_str) < LooseVersion("6.3.0"):
            assert_almost_equal((x2, y2), (1402291.0833290431, 5076289.591846835))
        else:
            # https://github.com/OSGeo/PROJ/issues/1808
>           assert_almost_equal((x2, y2), (1402285.9829252, 5076292.4212746))
E           AssertionError: 
E           Arrays are not almost equal to 7 decimals
E           
E           Mismatched elements: 2 / 2 (100%)
E           Max absolute difference: 4.21450818
E           Max relative difference: 1.82410064e-06
E            x: array([1402288.540836 , 5076296.6357828])
E            y: array([1402285.9829252, 5076292.4212746])

test/test_datum.py:20: AssertionError
_______________________________ test_datum[CRS] ________________________________

proj_class = <class 'pyproj.crs.crs.CRS'>, aoi_data_directory = None

    @pytest.mark.parametrize("proj_class", [Proj, CRS])
    def test_datum(proj_class, aoi_data_directory):
        p1 = proj_class(proj="latlong", datum="WGS84")
        s_1 = -111.5
        s_2 = 45.25919444444
        p2 = proj_class(proj="utm", zone=10, datum="NAD27")
        x2, y2 = transform(p1, p2, s_1, s_2)
        if LooseVersion(proj_version_str) < LooseVersion("6.3.0"):
            assert_almost_equal((x2, y2), (1402291.0833290431, 5076289.591846835))
        else:
            # https://github.com/OSGeo/PROJ/issues/1808
>           assert_almost_equal((x2, y2), (1402285.9829252, 5076292.4212746))
E           AssertionError: 
E           Arrays are not almost equal to 7 decimals
E           
E           Mismatched elements: 2 / 2 (100%)
E           Max absolute difference: 4.21450818
E           Max relative difference: 1.82410064e-06
E            x: array([1402288.540836 , 5076296.6357828])
E            y: array([1402285.9829252, 5076292.4212746])

test/test_datum.py:20: AssertionError
________________________________ test_doctests _________________________________

aoi_data_directory = None

    def test_doctests(aoi_data_directory):
        """run the examples in the docstrings using the doctest module"""
    
        with warnings.catch_warnings():
            warnings.filterwarnings(
                "ignore",
                "You will likely lose important projection information when",
                UserWarning,
            )
    
            failure_count_proj, test_count = doctest.testmod(pyproj.proj, verbose=True)
            failure_count_crs, test_count_crs = doctest.testmod(pyproj.crs, verbose=True)
            failure_count_geod, test_count_geod = doctest.testmod(pyproj.geod, verbose=True)
            failure_count_transform, test_count_transform = doctest.testmod(
                pyproj.transformer, verbose=True
            )
    
        failure_count = (
            failure_count_proj
            + failure_count_crs
            + failure_count_geod
            + failure_count_transform
        )
        # Missing shapely wheels for Windows, non x86_64 platforms, and python 3.8
        expected_failure_count = 0
        try:
            import shapely  # noqa
        except ImportError:
            if (
                os.name == "nt"
                or platform.uname()[4] != "x86_64"
                or (sys.version_info.major, sys.version_info.minor) >= (3, 8)
            ):
                expected_failure_count = 6
    
        # if the below line fails, doctests have failed
>       assert (
            failure_count == expected_failure_count
        ), "{0} of the doctests in " "lib/pyproj/__init__.py failed".format(failure_count)
E       AssertionError: 9 of the doctests in lib/pyproj/__init__.py failed
E       assert 9 == 6

test/test_doctest_wrapper.py:50: AssertionError

2 items had failures:
   3 of   5 in pyproj.geod.Geod.geometry_area_perimeter
   3 of   5 in pyproj.geod.Geod.geometry_length
2 items had failures:
   1 of   3 in pyproj.transformer.TransformerGroup.__init__
   2 of  19 in pyproj.transformer.transform

FAILED test/test_datum.py::test_datum[Proj] - AssertionError: 
FAILED test/test_datum.py::test_datum[CRS] - AssertionError: 
FAILED test/test_doctest_wrapper.py::test_doctests - AssertionError: 9 of the...
FAILED test/test_transformer.py::test_transform_wgs84_to_alaska - AssertionEr...
FAILED test/test_transformer.py::test_repr - AssertionError: assert '<Concate...
FAILED test/test_transformer.py::test_transformer_group__unavailable - assert...
FAILED test/test_transformer.py::test_transform_group__missing_best - assert ...
FAILED test/crs/test_crs.py::test_coordinate_operation_grids__alternative_grid_name

Expected Output

All tests passing =)

Environment Information

Shown in build log. Errors also occur on other architectures.

(9/39) Installing python3 (3.8.2-r0)
(17/39) Installing proj-datumgrid (7.0.0-r0)
(20/39) Installing proj (7.0.0-r0)
(21/39) Installing proj-dev (7.0.0-r0)

Installation method

From source
@russkel russkel added the bug label Mar 26, 2020
@snowman2 snowman2 added test Test related issues and removed bug labels Mar 26, 2020
@snowman2
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@russkel, all the failing tests are expected. Currently the tests are based on proj-datumgrid-1.8 as that is the last grid set that works with PROJ 6:

pyproj/ci/travis/proj-dl-and-compile

Line 12 in 57eeaf5

curl http://download.osgeo.org/proj/proj-datumgrid-1.8.zip > proj-datumgrid-1.8.zip

The failing tests are because the behavior is different with the new grids. I don't see any incorrect behavior from pyproj, so I think you are okay to proceed.

This will likely be addressed in #530, however the tests could also check for the existence of the new grids in the data directory for the tests.

@russkel
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russkel commented Mar 26, 2020

Hi @snowman2, thanks for your reply!

I just checked the proj build recipe (https://gitlab.alpinelinux.org/alpine/aports/blob/master/community/proj/APKBUILD) and it looks like it's still using the 1.8 datum grids as pyproj does. Am I misunderstanding?

@snowman2
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@russkel, that is interesting. I assumed you were using the latest grids. What is inside the proj-datumgrid package? It seems like that is installed separately and I am wondering if it is adding additional grids. I wonder if you run the tests without the proj-datumgrid package if the pyproj tests pass.

@snowman2
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Grids in the wheel:

$ unzip -l dist/pyproj-2.6.0-cp38-cp38-manylinux1_x86_64.whl
Archive:  dist/pyproj-2.6.0-cp38-cp38-manylinux1_x86_64.whl
  Length      Date    Time    Name
---------  ---------- -----   ----
... 
    7048  2020-03-18 00:51   pyproj/proj_dir/share/proj/stpaul
     6385  2020-03-18 00:51   pyproj/proj_dir/share/proj/nad.lst
   318464  2020-03-18 00:51   pyproj/proj_dir/share/proj/nzgd2kgrid0005.gsb
    19535  2020-03-18 00:51   pyproj/proj_dir/share/proj/nad27
    83696  2020-03-18 00:51   pyproj/proj_dir/share/proj/BETA2007.gsb
    11112  2020-03-18 00:51   pyproj/proj_dir/share/proj/WO
   277424  2020-03-18 00:51   pyproj/proj_dir/share/proj/ntf_r93.gsb
  1113184  2020-03-18 00:51   pyproj/proj_dir/share/proj/ntv1_can.dat
  1053928  2020-03-18 00:51   pyproj/proj_dir/share/proj/alaska
     7079  2020-03-18 00:51   pyproj/proj_dir/share/proj/world
   452008  2020-03-18 00:51   pyproj/proj_dir/share/proj/hawaii
     3660  2020-03-18 00:51   pyproj/proj_dir/share/proj/ITRF2008
  4153000  2020-03-18 00:51   pyproj/proj_dir/share/proj/egm96_15.gtx
    26728  2020-03-18 00:51   pyproj/proj_dir/share/proj/stlrnc
   264424  2020-03-18 00:51   pyproj/proj_dir/share/proj/conus
     2099  2020-03-18 00:51   pyproj/proj_dir/share/proj/ITRF2000
     1183  2020-03-18 00:51   pyproj/proj_dir/share/proj/CH
     3915  2020-03-18 00:51   pyproj/proj_dir/share/proj/other.extra
      232  2020-03-18 00:51   pyproj/proj_dir/share/proj/null
     3560  2020-03-18 00:51   pyproj/proj_dir/share/proj/MD
    32060  2020-03-18 00:51   pyproj/proj_dir/share/proj/projjson.schema.json
     6760  2020-03-18 00:51   pyproj/proj_dir/share/proj/WI
     4424  2020-03-18 00:51   pyproj/proj_dir/share/proj/TN
      728  2020-03-18 00:51   pyproj/proj_dir/share/proj/GL27
    26728  2020-03-18 00:51   pyproj/proj_dir/share/proj/prvi
    59208  2020-03-18 00:51   pyproj/proj_dir/share/proj/stgeorge
     3468  2020-03-18 00:51   pyproj/proj_dir/share/proj/ITRF2014
     8872  2020-03-18 00:51   pyproj/proj_dir/share/proj/FL
  6168576  2020-03-18 00:51   pyproj/proj_dir/share/proj/proj.db
    16593  2020-03-18 00:51   pyproj/proj_dir/share/proj/nad83
...   
---------                     -------
 25403377                     63 files

@snowman2
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Alpine linux package: https://pkgs.alpinelinux.org/contents?branch=edge&name=proj-datumgrid&arch=x86_64&repo=community


File | Package | Branch | Repository | Architecture
-- | -- | -- | -- | --
/usr/share/proj/proj.ini | proj-datumgrid | edge | community | x86_64
/usr/share/proj/ntf_r93.gsb | proj-datumgrid | edge | community | x86_64
/usr/share/proj/egm96_15.gtx | proj-datumgrid | edge | community | x86_64
/usr/share/proj/proj.db | proj-datumgrid | edge | community | x86_64
/usr/share/proj/CH | proj-datumgrid | edge | community | x86_64
/usr/share/proj/nad.lst | proj-datumgrid | edge | community | x86_64
/usr/share/proj/GL27 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/ITRF2008 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/nad83 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/ITRF2014 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/ITRF2000 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/nad27 | proj-datumgrid | edge | community | x86_64
/usr/share/proj/other.extra | proj-datumgrid | edge | community | x86_64
/usr/share/proj/nzgd2kgrid0005.gsb | proj-datumgrid | edge | community | x86_64
/usr/share/proj/world | proj-datumgrid | edge | community | x86_64
/usr/share/proj/BETA2007.gsb

Unless I am missing something (which is definitely possible), it looks like the alpine linux package is missing grids.

@snowman2
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v3.11 seems to have all of the grids: https://pkgs.alpinelinux.org/contents?file=&path=&name=proj-datumgrid&branch=v3.11&repo=community&arch=x86_64

Mind checking what is in your /usr/share/proj/ directory?

@russkel
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russkel commented Mar 27, 2020 •
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Mind checking what is in your /usr/share/proj/ directory?

This is a CI build, so it will be a fresh install. I will modify the build script to temporarily list the contents of that folder:

-rw-r--r--    1 root     root         83696 Mar  1 11:38 BETA2007.gsb
-rw-r--r--    1 root     root          1183 Mar  1 11:38 CH
-rw-r--r--    1 root     root           728 Mar  1 11:38 GL27
-rw-r--r--    1 root     root          2099 Mar  1 11:38 ITRF2000
-rw-r--r--    1 root     root          3660 Mar  1 11:38 ITRF2008
-rw-r--r--    1 root     root          3468 Mar  1 11:38 ITRF2014
-rw-r--r--    1 root     root       4153000 Mar  1 11:38 egm96_15.gtx
-rw-r--r--    1 root     root          6385 Mar  1 11:38 nad.lst
-rw-r--r--    1 root     root         19535 Mar  1 11:38 nad27
-rw-r--r--    1 root     root         16593 Mar  1 11:38 nad83
-rw-r--r--    1 root     root        277424 Mar  1 11:38 ntf_r93.gsb
-rw-r--r--    1 root     root        318464 Mar  1 11:38 nzgd2kgrid0005.gsb
-rw-r--r--    1 root     root          3915 Mar  1 11:38 other.extra
-rw-r--r--    1 root     root       6221824 Mar  1 11:38 proj.db
-rw-r--r--    1 root     root           354 Mar  1 11:38 proj.ini
-rw-r--r--    1 root     root          7079 Mar  1 11:38 world

I compared the edge and 3.11 (https://gitlab.alpinelinux.org/alpine/aports/blob/3.11-stable/community/proj/APKBUILD) build files for the datum grid package and they both use the same tar.gz with the same sha. It's possible I broke something when I 'fixed' the build script to build on all platforms, yiikes.

To answer your question, that package is built by moving /usr/share/proj into that package.

I will investigate further, thanks.

@russkel
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russkel commented Mar 27, 2020 •
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The only difference between proj in 3.11 and edge in this case is I switched to using CMake instead of autoconf. It's possible it's not installing all the gridfiles?

@snowman2
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Yes, I have had issues with missing grids using cmake in the past.

@russkel
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russkel commented Mar 27, 2020 •
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Yes, I have had issues with missing grids using cmake in the past.

Right. I will look into it. I thought CMake would have been the more relevant one to use 🤦‍♂️

@russkel
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russkel commented Mar 27, 2020 •
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Tests pass fine once I fixed the proj-datumgrid package. Sorry for wasting your time @snowman2 and thanks for your help!

pyproj should be merged into alpine edge soon.

@russkel russkel closed this as completed Mar 27, 2020
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