pygmt.show_versions: Show GMT binary version and hide the Python interpreter path #1838

seisman · 2022-03-21T13:09:19Z

Description of proposed changes

Show the GMT binary version available from the API parameter API_BIN_VERSION.
Don't show the GMT version by calling gmt --version
Don't show GMT's binary directory.

seisman · 2022-03-21T13:12:34Z

Here is the output when geopandas is not installed:

PyGMT information:
  version: v0.6.1.dev6+g813142bb.d20220321
System information:
  python: 3.9.5 (default, May 18 2021, 12:31:01)  [Clang 10.0.0 ]
  executable: /Users/user/opt/miniconda/bin/python
  machine: macOS-10.16-x86_64-i386-64bit
Dependency information:
  numpy: 1.21.4
  pandas: 1.3.4
  xarray: 0.20.1
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: None
  ghostscript: 9.55.0
GMT library information:
  cores: 8
  grid layout: rows
  library path: /Users/user/opt/GMT-master/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/user/opt/GMT-master/lib/gmt/plugins
  share dir: /Users/user/opt/GMT-master/share
  version: 6.4.0

When geopandas is installed:

PyGMT information:
  version: v0.6.1.dev6+g813142bb.d20220321
System information:
  python: 3.9.5 (default, May 18 2021, 12:31:01)  [Clang 10.0.0 ]
  executable: /Users/user/opt/miniconda/bin/python
  machine: macOS-10.16-x86_64-i386-64bit
Dependency information:
  numpy: 1.21.4
  pandas: 1.3.4
  xarray: 0.20.1
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: 0.10.2
  ghostscript: 9.55.0
GMT library information:
  cores: 8
  grid layout: rows
  library path: /Users/user/opt/GMT-master/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/user/opt/GMT-master/lib/gmt/plugins
  share dir: /Users/user/opt/GMT-master/share
  version: 6.4.0

weiji14 · 2022-03-25T13:18:26Z

pygmt/clib/session.py

        """
        if not hasattr(self, "_info"):
            self._info = {  # pylint: disable=attribute-defined-outside-init
                "version": self.get_default("API_VERSION"),


From #1830 (comment), you said:

2. The GMT version information gmt: 6.4.0_434ed18_2022.03.11 is obtained by calling gmt --version. However, when multiple GMT versions are installed, the command gmt and the library libgmt may come from different GMT versions. For example, if I have GMT 6.3 in my conda environment and GMT dev in another installation path, PyGMT may load the GMT 6.3 library but find GMT dev comman, or vice versa, depending on the settings of PATH and GMT_LIBRARY_PATH. It causes some confusion because PyGMT reports inconsistent GMT versions. I think we should remove the gmt: 6.4.0_434ed18_2022.03.11 information.

So we will only have 6.4.0 printed out. This is ok for most users who install the offficial release versions, but for those who install the dev versions, I think it's useful to have the git short-hash and date part too, so that we can know the exact GMT dev version we've installed.

Just as an idea, how about we check the two strings? If there are equal (e.g. 6.4.0 and 6.4.0), we just print one. But if they are different, then print both? Alternatively, is there a way to get the exact version from the GMT API somehow?

From #1830 (comment), you said:

The GMT version information gmt: 6.4.0_434ed18_2022.03.11 is obtained by calling gmt --version. However, when multiple GMT versions are installed, the command gmt and the library libgmt may come from different GMT versions. For example, if I have GMT 6.3 in my conda environment and GMT dev in another installation path, PyGMT may load the GMT 6.3 library but find GMT dev comman, or vice versa, depending on the settings of PATH and GMT_LIBRARY_PATH. It causes some confusion because PyGMT reports inconsistent GMT versions. I think we should remove the gmt: 6.4.0_434ed18_2022.03.11 information.

So we will only have 6.4.0 printed out. This is ok for most users who install the offficial release versions, but for those who install the dev versions, I think it's useful to have the git short-hash and date part too, so that we can know the exact GMT dev version we've installed.

Yes, I agree.

Just as an idea, how about we check the two strings? If there are equal (e.g. 6.4.0 and 6.4.0), we just print one. But if they are different, then print both?

We still have the same problem. When multiple GMT versions are installed, we may load the libgmt from GMT version A and call GMT CLI from GMT version B.

Alternatively, is there a way to get the exact version from the GMT API somehow?

I just checked the GMT source code. It's impossible to get the version string 6.4.0_434ed18_2022.03.11 from GMT API.

Since we can know the GMT library path library path: /Users/user/opt/GMT-master/lib/libgmt.dylib, perhaps we can assume that the relative path to the GMT command is {library path}/../bin/gmt? Or we can ask GMT to report the version string 6.4.0_434ed18_2022.03.11 through GMT API?

Alternatively, is there a way to get the exact version from the GMT API somehow?

I just checked the GMT source code. It's impossible to get the version string 6.4.0_434ed18_2022.03.11 from GMT API.

Since we can know the GMT library path library path: /Users/user/opt/GMT-master/lib/libgmt.dylib, perhaps we can assume that the relative path to the GMT command is {library path}/../bin/gmt? Or we can ask GMT to report the version string 6.4.0_434ed18_2022.03.11 through GMT API?

Getting it through the GMT API seems like the most robust solution, rather than having to guess where the actual GMT binary PyGMT is using is located on the filesystem. Not sure if this is possible though to get the git hash information in C?

I refer to the git commit information often when debugging (while careful to not have GMT installed via conda), so I added this option to the GMT_Get_Default API function in GenericMappingTools/gmt#6493 so that we can keep this information in show_versions.

pygmt/__init__.py

seisman · 2022-04-02T04:44:42Z

I've updated this PR to show the GMT version from the API parameter API_BIN_VERSION. We can only merge this PR after we bump the required GMT version to 6.4.0.

seisman · 2022-07-07T05:37:19Z

We need to make it backward compatible with the old GMT versions if we decide to
follow the suggestions in #1991.

seisman · 2022-08-28T15:12:22Z

I've made the commit 8df1b55 to make sure the new show_versions() function is backward compatible with GMT 6.3.0.

Here are the outputs for different cases:

GMT 6.3.0 with geopandas

PyGMT information:
  version: v0.7.1.dev56+g0e1ec564.d20220823
System information:
  python: 3.10.4 | packaged by conda-forge | (main, Mar 24 2022, 17:43:32) [Clang 12.0.1 ]
  executable: /Users/seisman/opt/miniconda/envs/dev/bin/python
  machine: macOS-12.5.1-x86_64-i386-64bit
Dependency information:
  numpy: 1.22.4
  pandas: 1.4.2
  xarray: 2022.3.0
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: 0.10.2
  ghostscript: 9.54.0
GMT library information:
  cores: 8
  grid layout: rows
  library path: /Users/seisman/opt/miniconda/envs/dev/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/seisman/opt/miniconda/envs/dev/lib/gmt/plugins
  share dir: /Users/seisman/opt/miniconda/envs/dev/share/gmt
  version: 6.3.0

GMT 6.3.0 without geopandas

PyGMT information:
  version: v0.7.1.dev56+g0e1ec564.d20220823
System information:
  python: 3.10.4 | packaged by conda-forge | (main, Mar 24 2022, 17:43:32) [Clang 12.0.1 ]
  executable: /Users/seisman/opt/miniconda/envs/dev/bin/python
  machine: macOS-12.5.1-x86_64-i386-64bit
Dependency information:
  numpy: 1.22.4
  pandas: 1.4.2
  xarray: 2022.3.0
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: None
  ghostscript: 9.54.0
GMT library information:
  cores: 8
  grid layout: rows
  library path: /Users/seisman/opt/miniconda/envs/dev/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/seisman/opt/miniconda/envs/dev/lib/gmt/plugins
  share dir: /Users/seisman/opt/miniconda/envs/dev/share/gmt
  version: 6.3.0

GMT 6.5.0 (dev) with geopandas

PyGMT information:
  version: v0.7.1.dev56+g0e1ec564.d20220823
System information:
  python: 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:28:27)  [Clang 11.1.0 ]
  executable: /Users/seisman/opt/miniconda/bin/python
  machine: macOS-12.5.1-x86_64-i386-64bit
Dependency information:
  numpy: 1.22.4
  pandas: 1.4.2
  xarray: 2022.3.0
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: 0.11.0
  ghostscript: 9.56.1
GMT library information:
  binary version: 6.5.0_566ed34_2022.08.08
  cores: 8
  grid layout: rows
  library path: /Users/seisman/opt/GMT-master/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/seisman/opt/GMT-master/lib/gmt/plugins
  share dir: /Users/seisman/opt/GMT-master/share
  version: 6.5.0

GMT 6.5.0 (dev) without geopandas

PyGMT information:
  version: v0.7.1.dev56+g0e1ec564.d20220823
System information:
  python: 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:28:27)  [Clang 11.1.0 ]
  executable: /Users/seisman/opt/miniconda/bin/python
  machine: macOS-12.5.1-x86_64-i386-64bit
Dependency information:
  numpy: 1.22.4
  pandas: 1.4.2
  xarray: 2022.3.0
  netCDF4: 1.5.8
  packaging: 21.3
  geopandas: None
  ghostscript: 9.56.1
GMT library information:
  binary version: 6.5.0_566ed34_2022.08.08
  cores: 8
  grid layout: rows
  library path: /Users/seisman/opt/GMT-master/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/seisman/opt/GMT-master/lib/gmt/plugins
  share dir: /Users/seisman/opt/GMT-master/share
  version: 6.5.0

weiji14 · 2022-09-09T16:08:50Z

pygmt/clib/session.py

+            if Version(self._info["version"]) >= Version("6.4.0"):
+                self._info["binary version"] = self.get_default("API_BIN_VERSION")


Is the binary version supposed to be just 6.4.0 (with no hash or date) for the official GMT 6.4 conda-forge package added in conda-forge/gmt-feedstock#212? I was expecting a string like 6.4.0_434ed18_2022.03.11, but am getting this output from python -c 'import pygmt; pygmt.show_versions()'

PyGMT information: version: v0.7.1.dev92+gde7026137 System information: python: 3.10.5 | packaged by conda-forge | (main, Jun 14 2022, 07:04:59) [GCC 10.3.0] executable: /home/username/mambaforge/envs/pygmt/bin/python machine: Linux-5.17.0-1016-oem-x86_64-with-glibc2.35 Dependency information: numpy: 1.23.2 pandas: 1.4.3 xarray: 2022.6.0 netCDF4: 1.6.0 packaging: 21.3 geopandas: 0.11.1 ghostscript: 9.54.0 GMT library information: binary version: 6.4.0 cores: 12 grid layout: rows library path: /home/username/mambaforge/envs/pygmt/lib/libgmt.so padding: 2 plugin dir: /home/username/mambaforge/envs/pygmt/lib/gmt/plugins share dir: /home/username/mambaforge/envs/pygmt/share/gmt version: 6.4.0

and output of mamba list | grep gmt is:

dcw-gmt 2.1.1 ha770c72_0 conda-forge gmt 6.4.0 h78e8b95_2 conda-forge gshhg-gmt 2.3.7 ha770c72_1003 conda-forge pygmt 0.7.1.dev92+gde7026137 pypi_0 pypi

Is the binary version supposed to be just 6.4.0 (with no hash or date) for the official GMT 6.4 conda-forge package added in conda-forge/gmt-feedstock#212? I was expecting a string like 6.4.0_434ed18_2022.03.11.

For official releases, the version string is 6.4.0 without hash and date. 6.4.0_434ed18_2022.03.11 is the version string for dev versions.

weiji14 · 2022-09-09T16:44:24Z

pygmt/tests/test_clib.py

+        if name == b"API_VERSION":
+            value.value = b"1.2.3"
+        else:
+            value.value = b"bla"
        return 0

    ses = clib.Session()
    ses.create("test-session")
    with mock(ses, "GMT_Get_Default", mock_func=mock_defaults):
        # Check for an empty dictionary
        assert ses.info
-        for value in ses.info.values():
-            assert value == "bla"
+        for key, value in ses.info.items():
+            if key == "version":
+                assert value == "1.2.3"
+            else:
+                assert value == "bla"


Should there also be a mock for if name == b"API_BIN_VERSION" and if key == "binary_version"? Or would that break with #2079?

At line 173 in pygmt/clib/session.py, we have the following code:

if Version(self._info["version"]) >= Version("6.4.0"): self._info["binary version"] = self.get_default("API_BIN_VERSION")

The Version() class requires self._info["version"] being a valid version string, so we can't give a value like bla to API_VERSION.

There is no such problem for API_BIN_VERSION, so no special operation is done for it.

…rpreter path (GenericMappingTools#1838)

seisman added the maintenance Boring but important stuff for the core devs label Mar 21, 2022

seisman added this to the 0.6.1 milestone Mar 21, 2022

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seisman mentioned this pull request Mar 25, 2022

Let pygmt.show_versions() report geopandas version #1846

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seisman marked this pull request as draft March 25, 2022 14:32

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seisman changed the title ~~Add geopandas version and remove GMT binary path and version from pygmt.show_versions()~~ Remove GMT binary path and version from pygmt.show_versions() Mar 26, 2022

maxrjones mentioned this pull request Mar 28, 2022

Add option to get Git commit information through C API GenericMappingTools/gmt#6493

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seisman added the upstream Bug or missing feature of upstream core GMT label Mar 29, 2022

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seisman added 2 commits April 2, 2022 11:13

Show geopandas version and remove GMT binary version

83242e9

Get API_BIN_VERSION

3dfae7b

seisman force-pushed the improve-show_versions branch from c8f7282 to 3dfae7b Compare April 2, 2022 04:41

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seisman added 2 commits August 28, 2022 23:05

Merge branch 'main' into improve-show_versions

9b16f59

Make sure it still works with GMT 6.3

8df1b55

seisman marked this pull request as ready for review August 28, 2022 15:12

seisman added the needs review This PR has higher priority and needs review. label Aug 28, 2022

seisman marked this pull request as draft August 28, 2022 15:47

seisman removed the needs review This PR has higher priority and needs review. label Aug 28, 2022

Fix a failing test due to invalid version string

05e2394

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seisman added the needs review This PR has higher priority and needs review. label Aug 28, 2022

seisman changed the title ~~Remove GMT binary path and version from pygmt.show_versions()~~ Improve pygmt.show_versions() to show GMT binary Remove GMT binary path and version from pygmt.show_versions() Aug 29, 2022

seisman changed the title ~~Improve pygmt.show_versions() to show GMT binary Remove GMT binary path and version from pygmt.show_versions()~~ pygmt.show_versions: Show GMT binary version and don't show the Python interpreter path Aug 29, 2022

seisman changed the title ~~pygmt.show_versions: Show GMT binary version and don't show the Python interpreter path~~ Improve pygmt.show_versions to show GMT binary version and hide the Python interpreter path Aug 29, 2022

seisman changed the title ~~Improve pygmt.show_versions to show GMT binary version and hide the Python interpreter path~~ pygmt.show_versions: Show GMT binary version and hide the Python interpreter path Aug 29, 2022

seisman added 2 commits September 2, 2022 22:39

Merge branch 'main' into improve-show_versions

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Merge branch 'main' into improve-show_versions

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Merge branch 'main' into improve-show_versions

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seisman merged commit 3e90b26 into main Sep 15, 2022

seisman deleted the improve-show_versions branch September 15, 2022 09:20

sixy6e pushed a commit to sixy6e/pygmt that referenced this pull request Dec 21, 2022

pygmt.show_versions: Show GMT binary version and hide the Python inte…

dbcaee7

…rpreter path (GenericMappingTools#1838)

		if Version(self._info["version"]) >= Version("6.4.0"):
		self._info["binary version"] = self.get_default("API_BIN_VERSION")

pygmt.show_versions: Show GMT binary version and hide the Python interpreter path #1838

pygmt.show_versions: Show GMT binary version and hide the Python interpreter path #1838

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seisman commented Aug 28, 2022

GMT 6.3.0 with geopandas

GMT 6.3.0 without geopandas

GMT 6.5.0 (dev) with geopandas

GMT 6.5.0 (dev) without geopandas

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seisman commented Mar 21, 2022 •

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