Merge branch 'SCECcode:main' into master

SCECcode · Feb 27, 2024 · edb49f6 · edb49f6
2 parents 9a71bfe + b3895d1
commit edb49f6
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diff --git a/.github/workflows/build-sphinx-no-deploy.yml b/.github/workflows/build-sphinx-no-deploy.yml
@@ -2,7 +2,7 @@ name: build-docs
 
 on:
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build_docs:

diff --git a/.github/workflows/build-sphinx.yml b/.github/workflows/build-sphinx.yml
@@ -2,7 +2,7 @@ name: docs
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build_docs:
@@ -39,6 +39,9 @@ jobs:
           doc_root=`mktemp -d`
           rsync -av "docs/_build/html/" "${doc_root}/"
           pushd "${doc_root}"
+          echo "${doc_root}"
+          echo "${GITHUB_ACTOR}"
+          echo "${GITHUB_REPOSITORY}"
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
           git init
@@ -47,5 +50,5 @@ jobs:
           echo "Empty README.md for documenation cache." > README.md
           echo "docs.cseptesting.org" > CNAME
           git add .
-          git commit -am "Updating pyCSEP docs for commit ${GITHUB_SHA} made on `date -d"@{SOURCE_DATE_EPOCH} --iso-8601=seconds` from ${GITHUB_REF} by ${GITHUB_ACTOR}"
+          git commit -am "Updating pyCSEP docs for commit ${GITHUB_SHA} from ${GITHUB_REF} by ${GITHUB_ACTOR}"
           git push deploy gh-pages --force
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -15,6 +15,9 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: ['3.7', '3.8', '3.9', '3.10']
+        include:
+          - os: windows-latest
+            python-version: '3.10'
     defaults:
       run:
         shell: bash -l {0}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,14 +1,32 @@
+# v0.6.3 (2/1/2024)
+
+# Change-log
+
+Added test for Winodws 10 on GitHub actions ([#244](https://github.com/SCECcode/pycsep/pull/244))  
+Removed shading in plotting fewer than 3 forecasts ([#247](https://github.com/SCECcode/pycsep/pull/247))  
+Fixed tutorial for plot_customizations ([#242](https://github.com/SCECcode/pycsep/pull/242))  
+Fixed negative binomial consistency plots now have the correct boundaries ([#245](https://github.com/SCECcode/pycsep/pull/245))  
+Changed environment build of pypi-publish from miniconda to micromamba ([#238](https://github.com/SCECcode/pycsep/pull/238))  
+Fixed negative timestamps parsing for Windows ([#230](https://github.com/SCECcode/pycsep/pull/230))  
+Fixed writing catalog csv files on Windows ([#235](https://github.com/SCECcode/pycsep/pull/235))
+
+## Credits
+Pablo Iturrieta (@pabloitu)  
+William Savran (@wsavran)  
+Philip Maechling (@pjmaechling)  
+Fabio Silva (@fabiolsilva)
+
 # v0.6.2 (6/16/2023)
 
 # Change-log
-Fixed an error-bar bug for normalized consistency plots ([#222](https://github.com/SCECcode/pycsep/pull/222))
-Fixed handles URL exception or SSL verifications errors for both python 3.8 and 3.11 inclusive ([#231](https://github.com/SCECcode/pycsep/pull/231))
-Included CMT Catalog accessor ([#217](https://github.com/SCECcode/pycsep/pull/217))
+Fixed an error-bar bug for normalized consistency plots ([#222](https://github.com/SCECcode/pycsep/pull/222))  
+Fixed handles URL exception or SSL verifications errors for both python 3.8 and 3.11 inclusive ([#231](https://github.com/SCECcode/pycsep/pull/231))  
+Included CMT Catalog accessor ([#217](https://github.com/SCECcode/pycsep/pull/217))  
 Added NZ catalog reader ([#213](https://github.com/SCECcode/pycsep/pull/213))
 
 ## Credits
-Pablo Iturrieta (@pabloitu)
-Kenny Graham (@KennyGraham1)
+Pablo Iturrieta (@pabloitu)  
+Kenny Graham (@KennyGraham1)  
 Fabio Silva (@fabiolsilva)
 
 # v0.6.1 (12/12/2022)

diff --git a/codemeta.json b/codemeta.json
@@ -5,11 +5,11 @@
     "codeRepository": "https://github.com/SCECcode/pycsep.git",
     "dateCreated": "2021-10-31",
     "datePublished": "2020-10-20",
-    "dateModified": "2023-06-16",
+    "dateModified": "2024-02-01",
     "downloadUrl": "https://github.com/SCECcode/pycsep",
     "issueTracker": "https://github.com/SCECcode/pycsep/issues",
     "name": "pyCSEP",
-    "version": "v0.6.2",
+    "version": "v0.6.3",
     "description": "The pyCSEP Toolkit helps earthquake forecast model developers evaluate their forecasts with the goal of understanding earthquake predictability.",
     "applicationCategory": "Seismology",
     "developmentStatus": "active",

diff --git a/csep/_version.py b/csep/_version.py
@@ -1,2 +1,2 @@
-__version__ = "0.6.2"
+__version__ = "0.6.3"
 
diff --git a/csep/utils/plots.py b/csep/utils/plots.py
@@ -1758,9 +1758,9 @@ def plot_comparison_test(results_t, results_w=None, axes=None, plot_args=None):
                     markerfacecolor=facecolor, markeredgecolor=color,
                     markersize=markersize)
 
+    ax.set_xticks(numpy.arange(len(results_t)))
     ax.set_xticklabels([res.sim_name[0] for res in results_t],
                        rotation=xticklabels_rotation, fontsize=xlabel_fontsize)
-    ax.set_xticks(numpy.arange(len(results_t)))
     ax.set_xlabel(xlabel)
     ax.set_ylabel(ylabel, fontsize=ylabel_fontsize)
     ax.set_title(title)
@@ -1769,8 +1769,9 @@ def plot_comparison_test(results_t, results_w=None, axes=None, plot_args=None):
     ax.yaxis.set_major_locator(matplotlib.ticker.MaxNLocator(integer=True))
     ax.set_ylim([ylim[0], ylim[1]])
     ax.set_xlim([-0.5, len(results_t) - 0.5])
-    ax.bar(xTickPos, numpy.array([9999] * len(xTickPos)), bottom=-2000,
-           width=(xTickPos[1] - xTickPos[0]), color=['gray', 'w'], alpha=0.2)
+    if len(results_t) > 2:
+        ax.bar(xTickPos, numpy.array([9999] * len(xTickPos)), bottom=-2000,
+               width=(xTickPos[1] - xTickPos[0]), color=['gray', 'w'], alpha=0.2)
     fig.tight_layout()
 
     return ax
@@ -1856,9 +1857,9 @@ def plot_consistency_test(eval_results, normalize=False, axes=None,
             mean = res.test_distribution[1]
             upsilon = 1.0 - ((var - mean) / var)
             tau = (mean ** 2 / (var - mean))
-            phigh = scipy.stats.nbinom.ppf((1 - percentile / 100.) / 2., tau,
+            plow = scipy.stats.nbinom.ppf((1 - percentile / 100.) / 2., tau,
                                            upsilon)
-            plow = scipy.stats.nbinom.ppf(1 - (1 - percentile / 100.) / 2.,
+            phigh = scipy.stats.nbinom.ppf(1 - (1 - percentile / 100.) / 2.,
                                           tau, upsilon)
 
         # empirical distributions

diff --git a/docs/conf.py b/docs/conf.py
@@ -30,7 +30,7 @@
 # The short X.Y version
 version = 'v0.6'
 # The full version, including alpha/beta/rc tags
-release = 'v0.6.2'
+release = 'v0.6.3'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/getting_started/installing.rst b/docs/getting_started/installing.rst
@@ -98,9 +98,10 @@ We recommend using ``conda`` to install the development environment. ::
     cd pycsep
     conda env create -f requirements.yml
     conda activate csep-dev
-    pip install -e .
+    pip install -e .[all]
     # Allow sync with default repository
     git remote add upstream https://github.com/SCECCode/pycsep.git
 
+This ensures to have a clean installation of ``pyCSEP`` and the required developer dependencies (e.g., ``pytest``, ``sphinx``).
 Now you can pull from upstream using ``git pull upstream master`` to keep your copy of the repository in sync with the
 latest commits.
diff --git a/examples/tutorials/plot_customizations.py b/examples/tutorials/plot_customizations.py
@@ -107,7 +107,7 @@
 # We define the arguments and a global projection, centered at $lon=-180$
 
 plot_args = {'figsize': (10,6), 'coastline':True, 'feature_color':'black',
-             'projection': cartopy.crs.Robinson(central_longitude=-179.0),
+             'projection': cartopy.crs.Robinson(central_longitude=180.0),
              'title': forecast.name, 'grid_labels': False,
              'cmap': 'magma',
              'clabel': r'$\log_{10}\lambda\left(M_w \in [{%.2f},\,{%.2f}]\right)$ per '
@@ -120,8 +120,8 @@
 # internally the extent of the plot
 
 ax = plots.plot_spatial_dataset(numpy.log10(rate_sum), forecast.region,
-                                show=True, set_global=True,
-                                plot_args=plot_args)
+                               show=True, set_global=True,
+                               plot_args=plot_args)
 
 ####################################################################################################################################
 

diff --git a/tests/test_JmaCsvCatalog.py b/tests/test_JmaCsvCatalog.py
@@ -1,9 +1,7 @@
 import unittest
 import csep
-
-
+from csep.utils.time_utils import datetime_to_utc_epoch
 import os.path
-
 import numpy
 
 def get_datadir():
@@ -43,8 +41,9 @@ def test_JmaCsvCatalog_loading():
     # _datetimes.fill(numpy.nan)
 
     for _idx, _val in enumerate(_dummy):
-        _datetimes[_idx] = round(1000. * _val.timestamp())
+        _datetimes[_idx] = datetime_to_utc_epoch(_val)
 
     numpy.testing.assert_allclose(_datetimes, test_catalog.catalog['origin_time'],
                                   err_msg='timestamp mismatch',
-                                  verbose=True, rtol=0, atol=0)
+                                  verbose=True,
+                                  rtol=1e-3, atol=0)