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

weiji14 · 2022-03-25T13:18:26Z

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.

weiji14 · 2022-09-09T16:08:50Z

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

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.

-Original file line number
+Diff line change
@@ Expand Up / @@ -146,17 +146,6 @@ def _get_ghostscript_version(): @@
                     continue
             return None
-        def _get_gmt_version():
-            """
-            Get GMT version.
-            """
-            try:
-                return subprocess.check_output(
-                    ["gmt", "--version"], universal_newlines=True
-                ).strip()
-            except FileNotFoundError:
-                return None
         sys_info = {
             "python": sys.version.replace("\n", " "),
             "executable": sys.executable,
@@ Expand All / @@ -176,7 +165,6 @@ def _get_gmt_version(): @@
         for modname in deps:
             print(f"  {modname}: {_get_module_version(modname)}")
         print(f"  ghostscript: {_get_ghostscript_version()}")
-        print(f"  gmt: {_get_gmt_version()}")
         print_clib_info()
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -158,7 +158,8 @@ def info(self): @@
                 self._info = {  # pylint: disable=attribute-defined-outside-init
                     "version": self.get_default("API_VERSION"),
                     "padding": self.get_default("API_PAD"),
-                    "binary dir": self.get_default("API_BINDIR"),
+                    # API_BINDIR points to the directory of the Python interpreter
+                    # "binary dir": self.get_default("API_BINDIR"),
                     "share dir": self.get_default("API_SHAREDIR"),
                     # This segfaults for some reason
                     # 'data dir': self.get_default("API_DATADIR"),
@@ Expand All / @@ -169,6 +170,9 @@ def info(self): @@
                     # "image layout": self.get_default("API_IMAGE_LAYOUT"),
                     "grid layout": self.get_default("API_GRID_LAYOUT"),
                 }
+                # API_BIN_VERSION is new in GMT 6.4.0.
+                if Version(self._info["version"]) >= Version("6.4.0"):
+                    self._info["binary version"] = self.get_default("API_BIN_VERSION")
             return self._info
         def __enter__(self):
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
             """
             Put 'bla' in the value buffer.
             """
-            value.value = b"bla"
+            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"
         ses.destroy()
@@ Expand Down @@

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