ci specific test-script setup (eqcorrscan#267)

* ci specific setup

* debug circleci

* debug circleci

* correct path

* sort coverage

* Verbose

* Verbose

* Verbose

* Verbose

* install not develop

* Put doctests in the right place

* Put appveyor in the right place

* Do not runslow if runsusperslow

* Remove old docs

* Update paths for appveyor

* Do not install to avoid ImportMismatchError with doctest-modules

* line endings?

* not installed script

* use develop

* use develop

* use more recent pytest

* Just use pytest the second time

* don't use test script on windows

* don't use test script on windows

* Fix paths and don't use symlink for testing

* Typo

* use real path

* full path for doc files

* Remove extraneous path bit

* Add doctest option

* do not pass doc arg to pytest

* expand paths

* test-data paths in docs

* Rewrite coveragerc with correct paths

* fix paths a bit more

* Use ret

* Linux doesn't like multiple conftests

* posix is different

* make context manager revert properly

* changelog

* Don't check milli seconds in rid

* Update PKG_PATH in conftest

* Update PKG_PATH in conftest

* Update PKG_PATH in conftest

.circleci/config.yml

@@ -48,19 +48,19 @@ jobs:
           command: |
             . venv/bin/activate
             python setup.py develop
-#            python setup.py build_ext --inplace
       # run tests!
       - run:
           name: run tests
           command: |
             . venv/bin/activate
-            test_eqcorrscan.py -m "network" -n 2
-            test_eqcorrscan.py eqcorrscan/doc/tutorials/*.rst eqcorrscan/doc/submodules/*.rst --cov-append
+            test_eqcorrscan.py --ci -m "network" -n 2
+            test_eqcorrscan.py --ci  --doc --cov-append
 
       - run:
           name: Upload to codecov
           command: |
             . venv/bin/activate
+            cp ~/.eqcorrscan/.coverage .
             ls -a
             codecov
 

.travis.yml

@@ -57,24 +57,24 @@ install:
   - conda list
   # done installing dependencies
   - git version
+#  - python setup.py install
   - python setup.py develop
-#  - python setup.py build_ext --inplace
 
 script:
    - export MPLBACKEND=Agg
-   - test_eqcorrscan.py --runslow -m "not serial and not network" -n 2
+   - test_eqcorrscan.py --ci --runslow -m "not serial and not network" -n 2
    #   - py.test --runslow -m "not serial and not network" -n 2
    - export OMP_NUM_THREADS=2;
    # These tests use multi-threading
    #   - py.test -m "serial and not network" --cov-append
-   - test_eqcorrscan.py -m "serial and not network" --cov-append
+   - test_eqcorrscan.py --ci -m "serial and not network" --cov-append
    #   - py.test --runsuperslow -s eqcorrscan/tests/tutorials_test.py --cov-append
-   - test_eqcorrscan.py --runsuperslow -s eqcorrscan/tests/tutorials_test.py --cov-append
+   - test_eqcorrscan.py --ci --runsuperslow -s --cov-append
 
 after_success:
   # Check how much code is actually tested and send this report to codecov
   - ls -a
-  - mv .coverage ../.coverage.empty
+  - mv ~/.eqcorrscan/.coverage ../.coverage.empty
   - cd ..
   - coverage combine
   - codecov

CHANGES.md

@@ -1,4 +1,7 @@
 ## Current
+* Make test-script more stable.
+* Fix bug where `set_xcorr` as context manager did not correctly reset
+  stream_xcorr methods.
 * Correct test-script (`test_eqcorrscan.py`) to find paths properly.
 
 ## 0.3.2

appveyor.yml

@@ -52,7 +52,7 @@ install:
 
   # Install other pip dependancies
   - "pip install -U future"
-  - "pip install pytest==3.2.4 pytest-pep8 pytest-cov pytest-xdist pytest-rerunfailures pytest-mpl codecov"
+  - "pip install pytest pytest-pep8 pytest-cov pytest-xdist pytest-rerunfailures pytest-mpl codecov"
   # list package versions
   - "conda list"
   # Copy the windows fftw header file
@@ -62,15 +62,13 @@ install:
 build: false
 
 test_script:
-  - "%CMD_IN_ENV% python setup.py build_ext --inplace"
   - "%CMD_IN_ENV% python setup.py develop"
-  - "%CMD_IN_ENV% test_eqcorrscan.py -n4 -m \"not serial and not network\""
-  - "%CMD_IN_ENV% test_eqcorrscan.py -m \"serial and not network\" --cov-append"
-#  - "%CMD_IN_ENV% test_eqcorrscan.py -n4 -m \"network\" --cov-append"
+#  - "%CMD_IN_ENV% python setup.py install"
+  - "%CMD_IN_ENV% py.test -n4 -m \"not serial and not network\""
+  - "%CMD_IN_ENV% py.test -m \"serial and not network\" --cov-append"
 
 after_test:
   #  - "coverage combine"
  #  - "powershell copy-item .coverage ..\\.coverage.empty"
- #  - "cd .."
  #  - "coverage combine"
   - "codecov"

eqcorrscan/core/match_filter.py

@@ -2037,8 +2037,12 @@ def construct(self, method, name, lowcut, highcut, samp_rate, filt_order,
 
         .. rubric:: Example
 
-        >>> sac_files = glob.glob(
-        ...     'eqcorrscan/tests/test_data/SAC/2014p611252/*')
+        >>> # Get the path to the test data
+        >>> import eqcorrscan
+        >>> import os
+        >>> TEST_PATH = (
+        ...     os.path.dirname(eqcorrscan.__file__) + '/tests/test_data')
+        >>> sac_files = glob.glob(TEST_PATH + '/SAC/2014p611252/*')
         >>> template = Template().construct(
         ...     method='from_sac', name='test', lowcut=2.0, highcut=8.0,
         ...     samp_rate=20.0, filt_order=4, prepick=0.1, swin='all',

eqcorrscan/core/template_gen.py

@@ -191,9 +191,13 @@ def template_gen(method, lowcut, highcut, samp_rate, filt_order,
 
     >>> from obspy import read
     >>> from eqcorrscan.core.template_gen import template_gen
-    >>> st = read('eqcorrscan/tests/test_data/WAV/TEST_/' +
+    >>> # Get the path to the test data
+    >>> import eqcorrscan
+    >>> import os
+    >>> TEST_PATH = os.path.dirname(eqcorrscan.__file__) + '/tests/test_data'
+    >>> st = read(TEST_PATH + '/WAV/TEST_/' +
     ...           '2013-09-01-0410-35.DFDPC_024_00')
-    >>> quakeml = 'eqcorrscan/tests/test_data/20130901T041115.xml'
+    >>> quakeml = TEST_PATH + '/20130901T041115.xml'
     >>> templates = template_gen(
     ...    method='from_meta_file', meta_file=quakeml, st=st, lowcut=2.0,
     ...    highcut=9.0, samp_rate=20.0, filt_order=3, length=2, prepick=0.1,
@@ -212,7 +216,7 @@ def template_gen(method, lowcut, highcut, samp_rate, filt_order,
     >>> from eqcorrscan.core.template_gen import template_gen
     >>> import glob
     >>> # Get all the SAC-files associated with one event.
-    >>> sac_files = glob.glob('eqcorrscan/tests/test_data/SAC/2014p611252/*')
+    >>> sac_files = glob.glob(TEST_PATH + '/SAC/2014p611252/*')
     >>> templates = template_gen(
     ...    method='from_sac', sac_files=sac_files, lowcut=2.0, highcut=10.0,
     ...    samp_rate=25.0, filt_order=4, length=2.0, swin='all', prepick=0.1,
@@ -1130,8 +1134,12 @@ def from_sac(sac_files, lowcut, highcut, samp_rate, filt_order, length, swin,
 
     >>> from eqcorrscan.core.template_gen import from_sac
     >>> import glob
+    >>> # Get the path to the test data
+    >>> import eqcorrscan
+    >>> import os
+    >>> TEST_PATH = os.path.dirname(eqcorrscan.__file__) + '/tests/test_data'
     >>> # Get all the SAC-files associated with one event.
-    >>> sac_files = glob.glob('eqcorrscan/tests/test_data/SAC/2014p611252/*')
+    >>> sac_files = glob.glob(TEST_PATH + '/SAC/2014p611252/*')
     >>> templates = from_sac(sac_files=sac_files, lowcut=2.0, highcut=10.0,
     ...                      samp_rate=25.0, filt_order=4, length=2.0,
     ...                      swin='all', prepick=0.1, all_horiz=True)
@@ -1226,9 +1234,13 @@ def from_meta_file(meta_file, st, lowcut, highcut, samp_rate, filt_order,
 
     >>> from obspy import read
     >>> from eqcorrscan.core.template_gen import from_meta_file
-    >>> st = read('eqcorrscan/tests/test_data/WAV/TEST_/' +
+    >>> # Get the path to the test data
+    >>> import eqcorrscan
+    >>> import os
+    >>> TEST_PATH = os.path.dirname(eqcorrscan.__file__) + '/tests/test_data'
+    >>> st = read(TEST_PATH + '/WAV/TEST_/' +
     ...           '2013-09-01-0410-35.DFDPC_024_00')
-    >>> quakeml = 'eqcorrscan/tests/test_data/20130901T041115.xml'
+    >>> quakeml = TEST_PATH + '/20130901T041115.xml'
     >>> templates = from_meta_file(meta_file=quakeml, st=st, lowcut=2.0,
     ...                            highcut=9.0, samp_rate=20.0, filt_order=3,
     ...                            length=2, prepick=0.1, swin='S',

eqcorrscan/doc/tutorials/clustering.rst

@@ -87,8 +87,10 @@ in the tests directory.
     >>> import glob
     >>> import os
     >>> from eqcorrscan.utils.clustering import cluster
+    >>> from eqcorrscan import tests
     >>> # You will need to edit this line to the location of your eqcorrscan repo.
-    >>> testing_path = 'eqcorrscan/tests/test_data/similar_events'
+    >>> TEST_PATH = os.path.dirname(tests.__file__)
+    >>> testing_path = TEST_PATH + '/test_data/similar_events'
     >>> stream_files = glob.glob(os.path.join(testing_path, '*'))
     >>> stream_list = [(read(stream_file), i)
     ...                for i, stream_file in enumerate(stream_files)]

eqcorrscan/doc/tutorials/mag-calc.rst

@@ -18,8 +18,10 @@ This example requires data downloaded from the eqcorrscan github repository.
     >>> from eqcorrscan.utils.mag_calc import amp_pick_event
     >>> from obspy import read, read_events
     >>> from obspy.io.nordic.core import readwavename
+    >>> from eqcorrscan import tests
     >>> import os
-    >>> testing_path = 'eqcorrscan/tests/test_data'
+    >>> # Get the path for the test-data so we can test this
+    >>> testing_path = os.path.dirname(tests.__file__) + '/test_data'
     >>> sfile = os.path.join(testing_path, 'REA', 'TEST_',
     ...                      '01-0411-15L.S201309')
     >>> datapath = os.path.join(testing_path, 'WAV', 'TEST_')
@@ -50,8 +52,11 @@ This example requires data downloaded from the eqcorrscan github repository.
     >>> import glob
     >>> from eqcorrscan.utils.clustering import svd
     >>> import numpy as np
-    >>> # Do the set-up
-    >>> testing_path = 'eqcorrscan/tests/test_data/similar_events'
+    >>> from eqcorrscan import tests
+    >>> import os
+    >>> # Get the path for the test-data so we can test this
+    >>> testing_path = os.path.dirname(
+    ...     tests.__file__) + '/test_data/similar_events'
     >>> stream_files = glob.glob(os.path.join(testing_path, '*'))
     >>> stream_list = [read(stream_file) for stream_file in stream_files]
     >>> event_list = []

eqcorrscan/doc/tutorials/matched-filter.rst

@@ -66,7 +66,11 @@ event:
 
      >>> import glob
      >>> from eqcorrscan.core.match_filter import Template
-     >>> sac_files = glob.glob('eqcorrscan/tests/test_data/SAC/2014p611252/*')
+     >>> import os
+     >>> from eqcorrscan import tests
+     >>> # Get the path for the test-data so we can test this
+     >>> TEST_PATH = os.path.dirname(tests.__file__)
+     >>> sac_files = glob.glob(TEST_PATH + '/test_data/SAC/2014p611252/*')
      >>> # sac_files is now a list of all the SAC files for event id:2014p611252
      >>> template = Template().construct(
      ...      method='from_sac', name='test', lowcut=2.0, highcut=8.0,

eqcorrscan/doc/tutorials/subspace.rst

@@ -64,7 +64,11 @@ aligned (see clustering submodule for alignment methods).
 
     >>> from obspy import read
     >>> import glob
-    >>> wavefiles = glob.glob('eqcorrscan/tests/test_data/similar_events/*')
+    >>> import os
+    >>> from eqcorrscan import tests
+    >>> # Get the path for the test-data so we can test this
+    >>> TEST_PATH = os.path.dirname(tests.__file__)
+    >>> wavefiles = glob.glob(TEST_PATH + '/test_data/similar_events/*')
     >>> wavefiles.sort()  # Sort the wavefiles to ensure reproducibility
     >>> streams = [read(w) for w in wavefiles[0:3]]
     >>> # Channels must all be the same length

eqcorrscan/scripts/test_eqcorrscan.py

@@ -30,7 +30,7 @@
 
 VERSION = eqcorrscan.__version__
 TEST_PATH = os.path.dirname(tests.__file__)
-PKG_PATH = os.path.dirname((eqcorrscan.__file__))
+PKG_PATH = os.path.dirname(eqcorrscan.__file__)
 WORKING_DIR = os.path.join(os.path.expanduser("~"), ".eqcorrscan")
 TAG_URL = "https://github.com/eqcorrscan/EQcorrscan/archive/{0}.zip".format(
     VERSION)
@@ -55,16 +55,38 @@ def __exit__(self, etype, value, traceback):
         os.chdir(self.savedPath)
 
 
+def setup_ci():
+    if not os.path.isdir(WORKING_DIR):
+        os.makedirs(WORKING_DIR)
+    for f in ["pytest.ini", "conftest.py"]:
+        shutil.copy(
+            os.path.join(os.getcwd(), f), WORKING_DIR)
+    check_path_conftest(os.path.join(WORKING_DIR, "conftest.py"))
+    rewrite_coveragerc(os.path.join(os.getcwd(), ".coveragerc"),
+                       os.path.join(WORKING_DIR, ".coveragerc"))
+    if os.path.isdir(TEST_DATA_PATH) and \
+       len(glob.glob(os.path.join(TEST_DATA_PATH, "*"))) == 0:
+        shutil.rmtree(TEST_DATA_PATH)
+    if not os.path.isdir(TEST_DATA_PATH):
+        test_data_path = os.path.join(
+            os.getcwd(), "eqcorrscan", "tests", "test_data")
+        shutil.copytree(test_data_path, TEST_DATA_PATH)
+    if os.path.isdir(os.path.join(PKG_PATH, "doc")) and \
+       len(glob.glob(os.path.join(PKG_PATH, "doc", "*"))) == 0:
+        shutil.rmtree(os.path.join(PKG_PATH, "doc"))
+    if not os.path.isdir(os.path.join(PKG_PATH, "doc")):
+        doc_path = os.path.join(
+            os.getcwd(), "eqcorrscan", "doc")
+        shutil.copytree(doc_path, os.path.join(PKG_PATH, "doc"))
+
+
 def download_test_data():
     """Check if test data are installed, and if not, download them"""
     test_data_downloaded = False
     control_files = [
         {"name": "pytest.ini", "downloaded": False},
         {"name": "conftest.py", "downloaded": False},
         {"name": ".coveragerc", "downloaded": False}]
-    pytest_ini_downloaded = False
-    conftest_downloaded = False
-    coveragerc_downloaded = False
     if os.path.isdir(TEST_DATA_PATH):
         if len(glob.glob(os.path.join(TEST_DATA_PATH, "*"))) > 0:
             Logger.info("Found test data at: {0}".format(TEST_DATA_PATH))
@@ -80,16 +102,12 @@ def download_test_data():
         os.makedirs(TEST_DATA_PATH)
     if not os.path.isdir(WORKING_DIR):
         os.makedirs(WORKING_DIR)
-    if not os.path.islink(os.path.join(WORKING_DIR, "eqcorrscan")):
-        # Make a symbolic link so that test data can be found
-        Logger.debug("Making symlink to install")
-        os.symlink(PKG_PATH, os.path.join(WORKING_DIR, "eqcorrscan"))
 
     control_files_downloaded = all([c["downloaded"] for c in control_files])
     if test_data_downloaded and control_files_downloaded:
         return
 
-    Logger.info("Downloading test data from github")
+    Logger.info("Downloading necessary files from github")
     with cd(TEST_DATA_PATH):
         # Get the whole zip for this release
         Logger.info("Downloading from {0}".format(TAG_URL))
@@ -107,7 +125,13 @@ def download_test_data():
                 contents.extract(extract_path, ".")
                 Logger.debug("Moving {0} to {1}".format(
                     extract_path, WORKING_DIR))
-                shutil.move(extract_path, WORKING_DIR)
+                if control_file["name"] == "conftest.py":
+                    check_path_conftest(extract_path)
+                if control_file["name"] == ".coveragerc":
+                    rewrite_coveragerc(
+                        extract_path, os.path.join(WORKING_DIR, ".coveragerc"))
+                else:
+                    shutil.move(extract_path, WORKING_DIR)
 
         if not test_data_downloaded:
             for file in contents.namelist():
@@ -122,21 +146,74 @@ def download_test_data():
     return
 
 
+def rewrite_coveragerc(infile, outfile):
+    with open(infile, "r") as f:
+        contents = f.read().split("\n")
+    with open(outfile, "w") as f:
+        for line in contents:
+            f.write(line.replace("eqcorrscan", PKG_PATH) + "\n")
+
+
+def check_path_conftest(conftest):
+    lines_out = []
+    with open(conftest, "r") as f:
+        for line in f:
+            if line.startswith("PKG_PATH"):
+                lines_out.append("PKG_PATH = '{0}'".format(PKG_PATH))
+            else:
+                lines_out.append(line)
+    with open(conftest, "w") as f:
+        for line in lines_out:
+            f.write(line + "\n")
+
+
 def run_tests(arg_list):
     """
     Run the tests.
     """
-    arg_list.extend(["--doctest-modules", "--runslow"])
+    # Convert arguments to real paths
+    if "--doc" in arg_list:
+        doc_files = glob.glob(
+            os.path.join(PKG_PATH, "doc", "tutorials", "*.rst"))
+        doc_files.extend(glob.glob(
+            os.path.join(PKG_PATH, "doc", "submodules", "*.rst")))
+        arg_list.extend(doc_files)
+        arg_list.remove("--doc")
+    elif "--runsuperslow" in arg_list:
+        arg_list.append(os.path.join(PKG_PATH, "tests", "tutorials_test.py"))
+    else:
+        arg_list.append(PKG_PATH)
+    if "--runsuperslow" not in arg_list and "--runslow" not in arg_list:
+        arg_list.append("--runslow")
     arg_list.extend(
-        ["--ignore", "EGG-INFO", "--ignore", "eqcorrscan/utils/lib"])
+        ["--ignore", "EGG-INFO", "--ignore", PKG_PATH + "/utils/lib",
+         "--doctest-modules", "--cov-config",
+         os.path.join(WORKING_DIR, ".coveragerc"), "--ignore=setup.py"])
     # arg_list.append(PKG_PATH)
     with cd(WORKING_DIR):
+        # If we are on windows, conftest.py has to be in the eqcorrscan dir :(
+        if sys.platform != "linux":
+            shutil.copy("pytest.ini", os.path.join(PKG_PATH, "pytest.ini"))
+            shutil.copy(".coveragerc", os.path.join(PKG_PATH, ".coveragerc"))
+            shutil.copy("conftest.py", os.path.join(PKG_PATH, "conftest.py"))
+        Logger.info("Working in {0}".format(WORKING_DIR))
         Logger.info("Running tests from {0}".format(PKG_PATH))
         Logger.info("pytest {0}".format(' '.join(arg_list)))
-        pytest.main(args=arg_list)
+        # Run the tests!
+        ret = pytest.main(args=arg_list)
+        if os.path.isfile(os.path.join(PKG_PATH, "conftest.py")):
+            os.remove(os.path.join(PKG_PATH, "pytest.ini"))
+            os.remove(os.path.join(PKG_PATH, ".coveragerc"))
+            os.remove(os.path.join(PKG_PATH, "conftest.py"))
+        if ret != 0:
+            raise SystemExit("Failed test")
 
 
 if __name__ == "__main__":
     arg_list = sys.argv[1:]
-    download_test_data()
+    if "--ci" in arg_list:
+        setup_ci()
+        arg_list.remove("--ci")
+    else:
+        download_test_data()
     run_tests(arg_list=arg_list)