Fix GDAL Python bindings and add import tests#8482
Merged
adamjstewart merged 1 commit intospack:developfrom Jun 15, 2018
Merged
Fix GDAL Python bindings and add import tests#8482adamjstewart merged 1 commit intospack:developfrom
adamjstewart merged 1 commit intospack:developfrom
Conversation
tgamblin
approved these changes
Jun 15, 2018
adamjstewart
force-pushed
the
packages/gdal-python
branch
from
9610fc1 to
cfaeda7
Compare
smuething
added a commit
to smuething/spack
that referenced
this pull request
Jun 18, 2018
* upstream-develop: (430 commits) There's only one 'u' in "configuration" (spack#8498) Add new versions for TAU and PDT package (spack#8497) Add changes to the Krell packages with version updates and ranges for the latest release. (spack#8468) docs: remove vendored sphinx_rtd_theme (spack#8496) Trilinos needs parallel-netcdf as an explicit dependency to avoid concretization errors when netcdf is an external. (spack#8493) superlu_dist: 'master' is branch - not tag (spack#8495) SAMRAI: new versions, handle deprecation of boost in latest version. (spack#8494) Fix GDAL Python bindings and add import tests (spack#8482) Add newer likwid versions 4.3.1 and 4.3.2 (spack#8488) Package/geopm: Update to version 0.5.0 (spack#8487) [mfem] Add BLAS+LAPACK to the required dependencies of SuperLU_DIST. (spack#8485) openssl: add new version 1.0.2o (spack#8486) Update the clang compiler definition to use IBM XL Fortran compiler (spack#8389) Patch trilinos for xlf when using clang (spack#8391) Use no mangling for all spack compiler definitions that use the XL (spack#8392) Use the name of the Fortran compiler to determine what name mangling (spack#8393) A new package: megahit. (spack#8471) neovim: add info for v0.3.0 (spack#8472) oce: add 0.18.3 (spack#8477) netgen should depend on zlib (spack#8473) ...
smuething
added a commit
to smuething/spack
that referenced
this pull request
Jun 18, 2018
* upstream-develop: (430 commits) There's only one 'u' in "configuration" (spack#8498) Add new versions for TAU and PDT package (spack#8497) Add changes to the Krell packages with version updates and ranges for the latest release. (spack#8468) docs: remove vendored sphinx_rtd_theme (spack#8496) Trilinos needs parallel-netcdf as an explicit dependency to avoid concretization errors when netcdf is an external. (spack#8493) superlu_dist: 'master' is branch - not tag (spack#8495) SAMRAI: new versions, handle deprecation of boost in latest version. (spack#8494) Fix GDAL Python bindings and add import tests (spack#8482) Add newer likwid versions 4.3.1 and 4.3.2 (spack#8488) Package/geopm: Update to version 0.5.0 (spack#8487) [mfem] Add BLAS+LAPACK to the required dependencies of SuperLU_DIST. (spack#8485) openssl: add new version 1.0.2o (spack#8486) Update the clang compiler definition to use IBM XL Fortran compiler (spack#8389) Patch trilinos for xlf when using clang (spack#8391) Use no mangling for all spack compiler definitions that use the XL (spack#8392) Use the name of the Fortran compiler to determine what name mangling (spack#8393) A new package: megahit. (spack#8471) neovim: add info for v0.3.0 (spack#8472) oce: add 0.18.3 (spack#8477) netgen should depend on zlib (spack#8473) ...
smuething
added a commit
to smuething/spack
that referenced
this pull request
Jun 18, 2018
* upstream-develop: (430 commits) There's only one 'u' in "configuration" (spack#8498) Add new versions for TAU and PDT package (spack#8497) Add changes to the Krell packages with version updates and ranges for the latest release. (spack#8468) docs: remove vendored sphinx_rtd_theme (spack#8496) Trilinos needs parallel-netcdf as an explicit dependency to avoid concretization errors when netcdf is an external. (spack#8493) superlu_dist: 'master' is branch - not tag (spack#8495) SAMRAI: new versions, handle deprecation of boost in latest version. (spack#8494) Fix GDAL Python bindings and add import tests (spack#8482) Add newer likwid versions 4.3.1 and 4.3.2 (spack#8488) Package/geopm: Update to version 0.5.0 (spack#8487) [mfem] Add BLAS+LAPACK to the required dependencies of SuperLU_DIST. (spack#8485) openssl: add new version 1.0.2o (spack#8486) Update the clang compiler definition to use IBM XL Fortran compiler (spack#8389) Patch trilinos for xlf when using clang (spack#8391) Use no mangling for all spack compiler definitions that use the XL (spack#8392) Use the name of the Fortran compiler to determine what name mangling (spack#8393) A new package: megahit. (spack#8471) neovim: add info for v0.3.0 (spack#8472) oce: add 0.18.3 (spack#8477) netgen should depend on zlib (spack#8473) ...
smuething
added a commit
to smuething/spack
that referenced
this pull request
Jun 18, 2018
* upstream-develop: (430 commits) There's only one 'u' in "configuration" (spack#8498) Add new versions for TAU and PDT package (spack#8497) Add changes to the Krell packages with version updates and ranges for the latest release. (spack#8468) docs: remove vendored sphinx_rtd_theme (spack#8496) Trilinos needs parallel-netcdf as an explicit dependency to avoid concretization errors when netcdf is an external. (spack#8493) superlu_dist: 'master' is branch - not tag (spack#8495) SAMRAI: new versions, handle deprecation of boost in latest version. (spack#8494) Fix GDAL Python bindings and add import tests (spack#8482) Add newer likwid versions 4.3.1 and 4.3.2 (spack#8488) Package/geopm: Update to version 0.5.0 (spack#8487) [mfem] Add BLAS+LAPACK to the required dependencies of SuperLU_DIST. (spack#8485) openssl: add new version 1.0.2o (spack#8486) Update the clang compiler definition to use IBM XL Fortran compiler (spack#8389) Patch trilinos for xlf when using clang (spack#8391) Use no mangling for all spack compiler definitions that use the XL (spack#8392) Use the name of the Fortran compiler to determine what name mangling (spack#8393) A new package: megahit. (spack#8471) neovim: add info for v0.3.0 (spack#8472) oce: add 0.18.3 (spack#8477) netgen should depend on zlib (spack#8473) ...
This was referenced Jun 22, 2018
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes #8469.
I accidentally broke our GDAL Python binding support in #8263 when I removed the
py-numpydependency. GDAL doesn't have great installation documentation, andnumpyisn't listed anywhere, so it got lost in the sea of dependencies. If you dig deep enough and read theswig/python/setup.pyfile, you'll see thatnumpyis an optional dependency needed to convert GeoTIFF files read by GDAL into numpy arrays.GDAL was also installing its Python bindings directly to the
site-packagesdirectory of the Python installation prefix, not to the GDAL installation prefix. This is now fixed.I also added import tests. If you run
spack install --test=root gdal+python, Spack will try to import commonosgeomodules. Hopefully this will catch things next time someone erroneously removespy-numpyfrom the dependency list.I also removed GDAL's swig dependency. Swig is needed to generate language bindings, but these bindings are already present in the downloaded tarball, so swig is not necessary.
Note: I encountered a couple of bugs while debugging this package. The first was #8475. For some reason, Spack was trying to apply the JasPer patch to GDAL even though I disabled JasPer support. I had to comment out the JasPer dependency to avoid this. The second was #987. Spack doesn't really support packages with multiple
extends()directives at the moment. In order to run the import tests, I needed to comment out theperldependency so that Spack could correctly detect that GDAL extends Python. I'm surprised that no one else encountered these problems.@neilflood. @michaelkuhn may also be interested in this.