Merge pull request #457 from eqcorrscan/develop

Merge for 0.4.3 release

Author: calum-chamberlain

.circleci/config.yml

@@ -3,24 +3,45 @@ on: [pull_request]  #, push]
 
 jobs:
   # Runs the tests on combinations of the supported python/os matrix.
-  test-code-macOS:
-    runs-on: "macos-latest"
+  test-code:
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: [3.7, 3.8]
       fail-fast: false
+#      continue-on-error: true
 
     steps:
       - uses: actions/checkout@v2
 
+      - name: Get conda env file
+        shell: bash -l {0}
+        run: |
+          if [ "$RUNNER_OS" == "macOS"  ]; then
+              cp .github/test_conda_env_macOS.yml .github/test_conda_env.yml
+          fi
+
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if needed by env file has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('.github/test_conda_env.yml') }}
+
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
           activate-environment: eqcorrscan-test
-          environment-file: .github/test_conda_env_macOS.yml
+          environment-file: .github/test_conda_env.yml
           condarc-file: .github/test_condarc.yml
+          use-only-tar-bz2: true  # Must be set for caching to work properly
 
       - name: install eqcorrscan
         shell: bash -l {0}
@@ -33,21 +54,32 @@ jobs:
           conda info -a
           conda list
 
+#      - name: run all tests
+#        shell: bash -l {0}
+#        run: |
+#          py.test -n 2 -m "not serial and not network and not superslow" --cov-report=xml
+#          export OMP_NUM_THREADS=2
+#          py.test -m "serial and not network" --cov-report=xml --cov-append
+#          py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append
+
       - name: run main test suite
         shell: bash -l {0}
-        continue-on-error: true
         run: |
           py.test -n 2 -m "not serial and not network and not superslow" --cov-report=xml
-      - name: run slow tests
-        shell: bash -l {0}
-        run: |
-          py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append
+
       - name: run serial test
+        if: always()
         shell: bash -l {0}
         run: |
           export OMP_NUM_THREADS=2
           py.test -m "serial and not network" --cov-report=xml --cov-append
 
+      - name: run slow tests
+        if: always()
+        shell: bash -l {0}
+        run: |
+          py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append
+
       - name: upload coverage
         uses: codecov/codecov-action@v1
         with:
@@ -58,16 +90,28 @@ jobs:
           yml: ./codecov.yml
           fail_ci_if_error: true
 
-  test-code-ubuntu:
+
+  test-code-slow:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8]
       fail-fast: false
 
     steps:
       - uses: actions/checkout@v2
 
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if needed by env file has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('.github/test_conda_env.yml') }}
+
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -76,6 +120,7 @@ jobs:
           activate-environment: eqcorrscan-test
           environment-file: .github/test_conda_env.yml
           condarc-file: .github/test_condarc.yml
+          use-only-tar-bz2: true  # Must be set for caching to work properly
 
       - name: install eqcorrscan
         shell: bash -l {0}
@@ -88,19 +133,20 @@ jobs:
           conda info -a
           conda list
 
-      - name: run main test suite
+      - name: run network tests
         shell: bash -l {0}
         run: |
-          py.test -n 2 -m "not serial and not network and not superslow" --cov-report=xml
-      - name: run slow tests
+          py.test -n 2 -m "network" --cov-report=xml
+      - name: run tutorials
+        if: always()
         shell: bash -l {0}
         run: |
-          py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append
-      - name: run serial test
+          py.test eqcorrscan/doc/tutorials/*.rst eqcorrscan/doc/submodules/*.rst --cov-report=xml --cov-append
+      - name: run superslow tests
+        if: always()
         shell: bash -l {0}
         run: |
-          export OMP_NUM_THREADS=2
-          py.test -m "serial and not network" --cov-report=xml --cov-append
+          py.test -m "superslow" -s eqcorrscan/tests/tutorials_test.py eqcorrscan/tests/subspace_test.py --cov-report=xml --cov-append
 
       - name: upload coverage
         uses: codecov/codecov-action@v1

.github/workflows/runtest.yml

@@ -1,5 +1,57 @@
-## Current
-
+## 0.4.3
+* core.match_filter
+ - match_filter:
+   - Provide option of exporting the cross-correlation sums for additional later
+     analysis.
+* core.match_filter.party.write
+  - BUG-FIX: When `format='tar'` is selected, added a check for .tgz-file
+    suffix before checking the filename against an existing file. Previously,
+    when a filename without '.tgz'-suffix was supplied, then the file was
+    overwritten against the function's intention.
+  - Add option `overwrite=True` to allow overwriting of existing files.
+* core.match_filter.party.read
+  - BUG-FIX: Ensure wildcard reading works as expected: #453
+* core.match_filter.party.rethreshold:
+  - added option to rethreshold based on absolute values to keep relevant
+    detections with large negative detect_val.
+* core.lag_calc:
+  - Added option to set minimum CC threshold individually for detections based
+    on: min(detect_val / n_chans * min_cc_from_mean_cc_factor, min_cc).
+  - Added the ability of saving correlation data of the lag_calc.
+* core.template_gen:
+  - Added support for generating templates from any object with a
+    get_waveforms method. See #459.
+* utils.mag_calc.calc_b_value:
+  - Added useful information to doc-string regarding method and meaning of
+    residuals
+  - Changed the number of magnitudes used to an int (from a string!?)
+* utils.mag_calc.relative_magnitude:
+  - Refactor so that `min_cc` is used regardless of whether 
+    `weight_by_correlation` is set. See issue #455.
+* utils.archive_read
+  - Add support for wildcard-comparisons in the list of requested stations and
+    channels.
+  - New option `arctype='SDS'` to read from a SeisComp Data Structure (SDS).
+    This option is also available in `utils.clustering.extract_detections` and
+    in `utils.archive_read._check_available_data`.
+* utils.catalog_to_dd
+  - Bug-fixes in #424:
+    - only P and S phases are used now (previously spurious amplitude picks 
+      were included in correlations);
+    - Checks for length are done prior to correlations and more helpful error
+      outputs are provided.
+    - Progress is not reported within dt.cc computation
+  - `write_station` now supports writing elevations: #424.
+* utils.clustering
+  - For `cluster`, `distance_matrix` and `cross_chan_correlation`, implemented
+    full support for `shift_len != 0`. The latter two functions now return, in
+    addition to the distance-matrix, a shift-matrix (both functions) and a
+    shift-dictionary (for `distance_matrix`). New option for shifting streams
+    as a whole or letting traces shift individually
+    (`allow_individual_trace_shifts=True`).
+* utils.plotting
+  - Function added (twoD_seismplot) for plotting seismicity (#365).
+  
 ## 0.4.2
 * Add seed-ids to the _spike_test's message.
 * utils.correlation

CHANGES.md

@@ -81,10 +81,8 @@ Note that tests for travis and appveyor are run daily on master as cron jobs, an
 
 | Service tests | Badge |
 |---------------|-------|
-| MacOS & Linux | ![test](https://github.com/eqcorrscan/EQcorrscan/workflows/test/badge.svg)
-| Windows | [![Build status](https://ci.appveyor.com/api/projects/status/6pp6jdop14hj4e63/branch/master?svg=true)](https://ci.appveyor.com/project/EQcorrscan/eqcorrscan/branch/master)
+| CI checks | ![test](https://github.com/eqcorrscan/EQcorrscan/workflows/test/badge.svg)
 | Code coverage | [![codecov](https://codecov.io/gh/eqcorrscan/EQcorrscan/branch/master/graph/badge.svg)](https://codecov.io/gh/eqcorrscan/EQcorrscan) 
-| Network tests | [![CircleCI](https://circleci.com/gh/eqcorrscan/EQcorrscan/tree/master.svg?style=svg)](https://circleci.com/gh/eqcorrscan/EQcorrscan/tree/master)
 
 # Licence
 

README.md

@@ -49,6 +49,7 @@ def clean_up_test_files():
         'test_waveforms.ms',
         'mag_calc.out',
         'station.dat',
+        'station_elev.dat',
         'test_waveform.ms',
         '01-0410-35L.S201309',
         '04-0007-55R.S201601',
@@ -83,6 +84,7 @@ def clean_up_test_directories():
         'test_party_out',
         'test_tar_write',
         'tmp1',
+        'cc_exported',
     ]
 
     yield

appveyor.yml

@@ -25,7 +25,7 @@
 
 __all__ = ['core', 'utils', 'tutorials', 'tests']
 
-__version__ = '0.4.2'
+__version__ = '0.4.3'
 
 # Cope with changes to name-space to remove most of the camel-case
 _import_map = {}