Log error messages with a callback instead of file

.stickler.yml

@@ -1,5 +1,6 @@
 linters:
     flake8:
+        python: 3
         enable: true
         ignore: E203, E266, E501, W503, F401, E741
         max-line-length: 88

.travis.yml

@@ -22,8 +22,7 @@ env:
         - BUILD_DOCS=false
         - DEPLOY_DOCS=false
         - DEPLOY_PYPI=false
-        # Need the dev channel to get development builds of GMT 6
-        - CONDA_FLAGS="--yes --quiet -c conda-forge -c conda-forge/label/dev"
+        - CONDA_REQUIREMENTS="requirements.txt"
 
 matrix:
     # Build under the following configurations
@@ -40,25 +39,24 @@ matrix:
               - BUILD_DOCS=true
               - DEPLOY_DOCS=true
               - DEPLOY_PYPI=true
-        #- os: osx
-          #env:
-              #- PYTHON=3.5
-        #- os: osx
-          #env:
-              #- PYTHON=3.6
-              #- COVERAGE=true
-              #- BUILD_DOCS=true
+        - os: osx
+          env:
+              - PYTHON=3.5
+              - BUILD_DOCS=true
+        - os: osx
+          env:
+              - PYTHON=3.6
+              - COVERAGE=true
+              - BUILD_DOCS=true
 
 before_install:
-    # Get Miniconda from Continuum
-    # Need to source the script to set the PATH variable in this environment
-    # (not the scripts environment)
-    - source ci/install-miniconda.sh
-    - conda update conda $CONDA_FLAGS
-    - conda create --name testenv python=$PYTHON pip $CONDA_FLAGS
-    - source activate testenv
-    # Install dependencies
-    - conda install --file requirements.txt $CONDA_FLAGS
+    # Get the Fatiando CI scripts
+    - git clone https://github.com/fatiando/continuous-integration.git
+    # Download and install miniconda and setup dependencies
+    # Need to source the script to set the PATH variable globaly
+    - source continuous-integration/travis/setup-miniconda.sh
+    # Install GMT from the dev channel to get development builds of GMT 6
+    - conda install --yes --quiet -c conda-forge/label/dev gmt=6.0.0a*
     - if [ "$COVERAGE" == "true" ]; then
         pip install codecov codacy-coverage codeclimate-test-reporter;
       fi
@@ -75,11 +73,11 @@ script:
     - if [ "$CHECK" == "true" ]; then
         make check;
       fi
-    # Run the test suite
+    # Run the test suite. Make pytest report any captured output on stdout or stderr.
     - if [ "$COVERAGE" == "true" ]; then
-        make coverage;
+        make coverage PYTEST_EXTRA="-r P";
       else
-        make test;
+        make test PYTEST_EXTRA="-r P";
       fi
     # Build the documentation
     - if [ "$BUILD_DOCS" == "true" ]; then
@@ -98,26 +96,26 @@ after_success:
       fi
 
 deploy:
-    # Push the built docs to Github pages
+    # Make a release on PyPI
     - provider: script
-      script: ci/deploy-docs.sh
+      script: continuous-integration/travis/deploy-pypi.sh
+      on:
+          tags: true
+          condition: '$DEPLOY_PYPI == "true"'
+    # Push the built HTML in doc/_build/html to the gh-pages branch
+    - provider: script
+      script: continuous-integration/travis/deploy-gh-pages.sh
       skip_cleanup: true
       on:
           branch: master
           condition: '$DEPLOY_DOCS == "true"'
-    # Push docs when building tags as well
+    # Push HTML when building tags as well
     - provider: script
-      script: ci/deploy-docs.sh
+      script: continuous-integration/travis/deploy-gh-pages.sh
       skip_cleanup: true
       on:
           tags: true
           condition: '$DEPLOY_DOCS == "true"'
-    # Make a release on PyPI
-    - provider: script
-      script: ci/deploy-pypi.sh
-      on:
-          tags: true
-          condition: '$DEPLOY_PYPI == "true"'
 
 notifications:
     email: false

gmt/clib/core.py

@@ -1,9 +1,8 @@
 """
 ctypes wrappers for core functions from the C API
 """
-import os
+import sys
 import ctypes
-from tempfile import NamedTemporaryFile
 from contextlib import contextmanager
 
 from packaging.version import Version
@@ -254,10 +253,26 @@ def create_session(self, session_name):
             restype=ctypes.c_void_p,
         )
 
-        # None is passed in place of the print function pointer. It becomes the
-        # NULL pointer when passed to C, prompting the C API to use the default
-        # print function.
-        print_func = None
+        # Capture the output printed by GMT into this list. Will use it later to
+        # generate error messages for the exceptions raised by API calls.
+        self._log = []
+
+        @ctypes.CFUNCTYPE(ctypes.c_int, ctypes.c_void_p, ctypes.c_char_p)
+        def print_func(file_pointer, message):  # pylint: disable=unused-argument
+            """
+            Callback function that GMT uses to print log and error messages.
+            We'll capture the message and print it to stderr so that it will show up on
+            the Jupyter notebook.
+            """
+            message = message.decode().strip()
+            self._log.append(message)
+            print(message, file=sys.stderr)
+            return 0
+
+        # Need to store a copy of the function because ctypes doesn't and it will be
+        # garbage collected otherwise
+        self._print_callback = print_func
+
         padding = self.get_constant("GMT_PAD_DEFAULT")
         session_type = self.get_constant("GMT_SESSION_EXTERNAL")
         session = c_create_session(
@@ -269,6 +284,16 @@ def create_session(self, session_name):
 
         return session
 
+    def _get_error_message(self):
+        """
+        Return a string with error messages emitted by GMT.
+        Only includes messages with the string "[ERROR]" in them.
+        """
+        msg = ""
+        if hasattr(self, "_log"):
+            msg = "\n".join(line for line in self._log if "[ERROR]" in line)
+        return msg
+
     def destroy_session(self, session):
         """
         Terminate and free the memory of a registered ``GMTAPI_CTRL`` session.
@@ -382,73 +407,6 @@ def get_default(self, name):
 
         return value.value.decode()
 
-    @contextmanager
-    def log_to_file(self, logfile=None):
-        """
-        Set the next API call in this session to log to a file.
-
-        Use it as a context manager (in a ``with`` block) to capture the error
-        messages from GMT API calls. Mostly useful with ``GMT_Call_Module``
-        because most others don't print error messages.
-
-        The log file will be deleted when exiting the ``with`` block.
-
-        Calls the GMT API function ``GMT_Handle_Messages`` using
-        ``GMT_LOG_ONCE`` mode (to only log errors from the next API call).
-        Only works for a **single API call**, so make calls like
-        ``get_constant`` outside of the ``with`` block.
-
-        Parameters
-        ----------
-        * logfile : str or None
-            The name of the logfile. If ``None`` (default),
-            the file name is automatically generated by the tempfile module.
-
-        Examples
-        --------
-
-        >>> with LibGMT() as lib:
-        ...     mode = lib.get_constant('GMT_MODULE_CMD')
-        ...     with lib.log_to_file() as logfile:
-        ...         call_module = lib.get_libgmt_func('GMT_Call_Module')
-        ...         status = call_module(lib.current_session, 'info'.encode(),
-        ...                              mode, 'bogus-file.bla'.encode())
-        ...         with open(logfile) as flog:
-        ...             print(flog.read().strip())
-        gmtinfo [ERROR]: Error for input file: No such file (bogus-file.bla)
-
-        """
-        c_handle_messages = self.get_libgmt_func(
-            "GMT_Handle_Messages",
-            argtypes=[ctypes.c_void_p, ctypes.c_uint, ctypes.c_uint, ctypes.c_char_p],
-            restype=ctypes.c_int,
-        )
-
-        if logfile is None:
-            tmp_file = NamedTemporaryFile(
-                prefix="gmt-python-", suffix=".log", delete=False
-            )
-            logfile = tmp_file.name
-            tmp_file.close()
-
-        status = c_handle_messages(
-            self.current_session,
-            self.get_constant("GMT_LOG_ONCE"),
-            self.get_constant("GMT_IS_FILE"),
-            logfile.encode(),
-        )
-        if status != 0:
-            msg = "Failed to set logging to file '{}' (error: {}).".format(
-                logfile, status
-            )
-            raise GMTCLibError(msg)
-
-        # The above is called when entering a 'with' statement
-        yield logfile
-
-        # Clean up when exiting the 'with' statement
-        os.remove(logfile)
-
     def call_module(self, module, args):
         """
         Call a GMT module with the given arguments.
@@ -479,30 +437,15 @@ def call_module(self, module, args):
         )
 
         mode = self.get_constant("GMT_MODULE_CMD")
-        # If there is no open session, this will raise an exception. Can' let
-        # it happen inside the 'with' otherwise the logfile won't be deleted.
-        session = self.current_session
-        with self.log_to_file() as logfile:
-            status = c_call_module(session, module.encode(), mode, args.encode())
-            # Get the error message inside the with block before the log file
-            # is deleted
-            with open(logfile) as flog:
-                log = flog.read().strip()
-        # Raise the exception outside the log 'with' to make sure the logfile
-        # is cleaned.
+        status = c_call_module(
+            self.current_session, module.encode(), mode, args.encode()
+        )
         if status != 0:
-            if log == "":
-                msg = "Invalid GMT module name '{}'.".format(module)
-            else:
-                msg = "\n".join(
-                    [
-                        "Command '{}' failed:".format(module),
-                        "---------- Error log ----------",
-                        log,
-                        "-------------------------------",
-                    ]
+            raise GMTCLibError(
+                "Module '{}' failed with status code {}:\n{}".format(
+                    module, status, self._get_error_message()
                 )
-            raise GMTCLibError(msg)
+            )
 
     def create_data(self, family, geometry, mode, **kwargs):
         """
@@ -1324,8 +1267,6 @@ def extract_region(self):
         )
 
         wesn = np.empty(4, dtype=np.float64)
-        # Use NaNs so that we can know if GMT didn't change the array
-        wesn[:] = np.nan
         wesn_pointer = wesn.ctypes.data_as(ctypes.POINTER(ctypes.c_double))
         # The second argument to GMT_Extract_Region is a file pointer to a
         # PostScript file. It's only valid in classic mode. Use None to get a