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Diff for: ‎.github/workflows/build_docs.yml

+6-2
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,10 @@ name: docs
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on:
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push:
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branches: [main]
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pull_request:
9+
branches: [main]
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workflow_dispatch:
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jobs:
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build:
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name: Build the documentation with Sphinx
@@ -29,13 +32,14 @@ jobs:
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- name: Build documentation
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run: sphinx-build documentation/ documentation/_build/html
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- name: Upload artifact
32-
uses: actions/upload-pages-artifact@v1
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uses: actions/upload-pages-artifact@v3
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with:
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path: 'documentation/_build/html'
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deploy:
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name: Deploy documentation to GitHub Pages
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needs: build
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if: github.event_name == 'push'
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permissions:
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contents: read
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pages: write # to deploy to Pages
@@ -49,4 +53,4 @@ jobs:
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uses: actions/configure-pages@v3
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v1
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uses: actions/deploy-pages@v4

Diff for: ‎.github/workflows/build_tests.yml

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@@ -13,12 +13,14 @@ on:
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jobs:
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16-
build:
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build_wheels:
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name: Build wheels
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
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os: [windows-latest, macOS-latest, ubuntu-latest]
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fail-fast: false
2224
steps:
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- uses: actions/checkout@v4
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- name: Set up Python
@@ -35,19 +37,21 @@ jobs:
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run: |
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python setup.py bdist_wheel
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ls dist/*
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- name: Save wheel
40+
- name: Upload wheels
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uses: actions/upload-artifact@v4
4042
with:
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name: pecos_${{ matrix.python-version }}_${{ matrix.os }}.whl
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path: dist/pecos*
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install_import:
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needs: build
46+
test_wheels:
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name: Test wheels
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needs: build_wheels
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
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os: [windows-latest, macOS-latest, ubuntu-latest]
54+
fail-fast: false
5155
steps:
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- name: Set up Python
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uses: actions/setup-python@v5
@@ -62,16 +66,17 @@ jobs:
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python -m pip install --upgrade pip
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pip install wheel numpy pandas jinja2 matplotlib pytest
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pip install --no-index --pre --find-links=. pecos
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- name: Usage of pecos
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- name: Import pecos
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run: |
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python -c "import pecos"
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pytest_coverage:
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run_coverage:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.9', '3.10', '3.11', '3.12']
7478
os: [windows-latest, macOS-latest, ubuntu-latest]
79+
fail-fast: false
7580
steps:
7681
- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
@@ -85,7 +90,7 @@ jobs:
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pip install -r requirements.txt
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python -m pip install -e .
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- name: Run Tests
88-
run: |
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run: |
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coverage erase
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coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" -m pytest --doctest-modules --doctest-glob="*.rst" pecos
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coverage run --context=${{ matrix.os }}.py${{ matrix.python-version }} --source=pecos --omit="*/tests/*" --append -m pytest --doctest-glob="*.rst" documentation
@@ -94,11 +99,12 @@ jobs:
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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name: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
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path: .coverage.${{ matrix.python-version }}.${{ matrix.os }}
104+
include-hidden-files: true
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100106
combine_reports:
101-
needs: [ pytest_coverage ]
107+
needs: [ run_coverage ]
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runs-on: ubuntu-latest
103109
steps:
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- name: Set up Python
@@ -111,11 +117,14 @@ jobs:
111117
python -m pip install --upgrade pip
112118
pip install -r requirements.txt
113119
python -m pip install -e .
120+
pip install coveralls
114121
- name: Download coverage artifacts from test matrix
115122
uses: actions/download-artifact@v4
116123
with:
117-
name: coverage
124+
pattern: .coverage.*.ubuntu-latest # coverage from other OS cause problems
118125
- name: Setup coverage and combine reports
126+
run: coverage combine .coverage.*.ubuntu-latest
127+
- name: Create coverage report
119128
run: |
120129
echo "[paths]" > .coveragerc
121130
echo "source = " >> .coveragerc
@@ -124,55 +133,21 @@ jobs:
124133
echo " D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
125134
echo " /home/runner/work/pecos/pecos/pecos" >> .coveragerc
126135
echo " /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
127-
coverage combine
128-
- name: Create coverage report
129-
run: |
136+
echo " ${{ github.workspace }}/pecos" >> .coveragerc
130137
coverage report
131138
coverage json --pretty-print
132139
coverage html --show-contexts
133140
- name: Save coverage JSON
134141
uses: actions/upload-artifact@v4
135142
with:
136-
name: coverage
143+
name: coverage-json
137144
path: coverage.json
138145
- name: Save coverage html
139146
uses: actions/upload-artifact@v4
140147
with:
141-
name: coverage
148+
name: coverage-html
142149
path: htmlcov
143-
144-
coveralls:
145-
needs: [ pytest_coverage ]
146-
runs-on: ubuntu-latest
147-
continue-on-error: true
148-
steps:
149-
- name: Set up Python
150-
uses: actions/setup-python@v5
151-
with:
152-
python-version: 3.11
153-
- uses: actions/checkout@v4
154-
- name: Install coverage
155-
run: |
156-
python -m pip install --upgrade pip
157-
pip install coveralls
158-
pip install -r requirements.txt
159-
python -m pip install -e .
160-
- name: Download coverage artifacts from test matrix
161-
uses: actions/download-artifact@v2
162-
with:
163-
name: coverage
164-
- name: Setup coverage and combine reports
165-
run: |
166-
echo "[paths]" > .coveragerc
167-
echo "source = " >> .coveragerc
168-
echo " pecos/" >> .coveragerc
169-
echo " pecos\\" >> .coveragerc
170-
echo " D:\\a\\pecos\\pecos\\pecos" >> .coveragerc
171-
echo " /home/runner/work/pecos/pecos/pecos" >> .coveragerc
172-
echo " /Users/runner/work/pecos/pecos/pecos" >> .coveragerc
173-
coverage combine
174150
- name: Push to coveralls
175-
run: |
176-
coveralls --service=github
151+
run: coveralls --service=github --rcfile=.coveragerc
177152
env:
178153
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Diff for: ‎.gitignore

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@@ -4,6 +4,8 @@
44
_build/
55
pecos.egg-info/*
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logfile
7+
build/
8+
dist/
79

810
*.html
911
*.csv

Diff for: ‎documentation/composite_signal.rst

+1-1
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@@ -36,7 +36,7 @@ the PerformanceMonitoring object.
3636
>>> import numpy as np
3737
>>> import pecos
3838
>>> pm = pecos.monitoring.PerformanceMonitoring()
39-
>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
39+
>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
4040
>>> data = {'A': np.arange(24)}
4141
>>> df = pd.DataFrame(data, index=index)
4242
>>> pm.add_dataframe(df)

Diff for: ‎documentation/metrics.rst

+1-1
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@@ -31,7 +31,7 @@ To compute QCI,
3131
>>> import numpy as np
3232
>>> import pecos
3333
>>> pm = pecos.monitoring.PerformanceMonitoring()
34-
>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
34+
>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
3535
>>> data = {'A': np.arange(24)}
3636
>>> df = pd.DataFrame(data, index=index)
3737
>>> pm.add_dataframe(df)

Diff for: ‎documentation/timefilter.rst

+1-1
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@@ -16,7 +16,7 @@ The following example defines a time filter between 3 AM and 9 PM,
1616
>>> import numpy as np
1717
>>> import pecos
1818
>>> pm = pecos.monitoring.PerformanceMonitoring()
19-
>>> index = pd.date_range('1/1/2017', periods=24, freq='H')
19+
>>> index = pd.date_range('1/1/2017', periods=24, freq='h')
2020
>>> data = {'A': np.arange(24)}
2121
>>> df = pd.DataFrame(data, index=index)
2222
>>> pm.add_dataframe(df)

Diff for: ‎documentation/whatsnew.rst

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@@ -1,6 +1,10 @@
11
Release Notes
22
================
33

4+
.. include:: whatsnew/v1.0.0.rst
5+
6+
.. include:: whatsnew/v0.3.1.rst
7+
48
.. include:: whatsnew/v0.3.0.rst
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.. include:: whatsnew/v0.2.0.rst

Diff for: ‎documentation/whatsnew/v0.3.0.rst

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@@ -1,6 +1,6 @@
11
.. _whatsnew_030:
22

3-
v0.3.0 (main)
3+
v0.3.0 (October 17, 2023)
44
--------------------------
55

66
* Bug fix in custom static and streaming quality control tests to use a specific column

Diff for: ‎documentation/whatsnew/v0.3.1.rst

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@@ -0,0 +1,7 @@
1+
.. _whatsnew_031:
2+
3+
v0.3.1 (October 27, 2023)
4+
--------------------------
5+
6+
* Relaxed dtype check in tests
7+
* Fixed import fail due to pytest ModuleNotFoundError

Diff for: ‎documentation/whatsnew/v1.0.0.rst

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@@ -0,0 +1,7 @@
1+
.. _whatsnew_100:
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Version 1.0.0 (main)
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--------------------------
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6+
* Updates to support Numpy2
7+

Diff for: ‎examples/dashboard/dashboard_example_1.py

+1-1
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@@ -40,7 +40,7 @@
4040

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# Populate the object with a dataframe and translation dictionary
4242
# In this example, fake data is generated using a sin wave function
43-
index = pd.date_range(analysis_date, periods=24, freq='H')
43+
index = pd.date_range(analysis_date, periods=24, freq='h')
4444
data=np.sin(np.random.rand(3,1)*np.arange(0,24,1))
4545
df = pd.DataFrame(data=data.transpose(), index=index, columns=['A', 'B', 'C'])
4646
pm.add_dataframe(df)

Diff for: ‎pecos/__init__.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
from pecos import utils
77
from pecos import pv
88

9-
__version__ = '0.3.1'
9+
__version__ = '1.0.0'
1010

1111
__copyright__ = """Copyright 2016 National Technology & Engineering
1212
Solutions of Sandia, LLC (NTESS). Under the terms of Contract

Diff for: ‎pecos/graphics.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -157,7 +157,7 @@ def plot_timeseries(data, tfilter=None, test_results_group=None, xaxis_min=None,
157157
temp = np.append(temp[0],len(tfilter)-1)
158158
count = 0
159159
for i in range(len(temp)-1):
160-
if tfilter[temp[i]] == 0:
160+
if tfilter.iloc[temp[i]] == 0:
161161
if count == 0:
162162
ax.axvspan(data.index[temp[i]], data.index[temp[i+1]],
163163
facecolor='k', alpha=0.2, label='Time filter')
@@ -399,7 +399,7 @@ def plot_doy_heatmap(data, cmap='nipy_spectral', vmin=None, vmax=None,
399399
data.index.minute + \
400400
data.index.second/60 + \
401401
data.index.microsecond/(60*1000000.0)
402-
piv = pd.pivot_table(data,values=col_name,index=['Y'],columns=['X'],fill_value=np.NaN)
402+
piv = pd.pivot_table(data,values=col_name,index=['Y'],columns=['X'],fill_value=np.nan)
403403

404404
# Create the heatmap
405405
plt.figure(figsize = figsize)

Diff for: ‎pecos/metrics.py

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@@ -9,7 +9,7 @@
99
logger = logging.getLogger(__name__)
1010

1111
def qci(mask, tfilter=None):
12-
"""
12+
r"""
1313
Compute the quality control index (QCI) for each column, defined as:
1414
1515
:math:`QCI=\dfrac{\sum_{t\in T}X_{dt}}{|T|}`
@@ -42,7 +42,7 @@ def qci(mask, tfilter=None):
4242
return qci
4343

4444
def rmse(data1, data2, tfilter=None):
45-
"""
45+
r"""
4646
Compute the root mean squared error (RMSE) for each column, defined as:
4747
4848
:math:`RMSE=\sqrt{\dfrac{\sum{(data_1-data_2)^2}}{n}}`
@@ -86,15 +86,15 @@ def rmse(data1, data2, tfilter=None):
8686
return rmse
8787

8888
def time_integral(data, tfilter=None):
89-
"""
89+
r"""
9090
Compute the time integral (F) for each column, defined as:
9191
9292
:math:`F=\int{fdt}`
9393
9494
where
9595
:math:`f` is a column of data
9696
:math:`dt` is the time step between observations.
97-
The integral is computed using the trapezoidal rule from numpy.trapz.
97+
The integral is computed using the trapezoidal rule from numpy.trapezoid.
9898
Results are given in [original data units]*seconds.
9999
NaN values are set to 0 for integration.
100100
@@ -124,14 +124,14 @@ def time_integral(data, tfilter=None):
124124

125125
F = {}
126126
for col in data.columns:
127-
F[col] = float(np.trapz(data.loc[:,col], tdelta))
127+
F[col] = float(np.trapezoid(data.loc[:,col], tdelta))
128128

129129
F = pd.Series(F)
130130

131131
return F
132132

133133
def time_derivative(data, tfilter=None):
134-
"""
134+
r"""
135135
Compute the derivative (f') of each column, defined as:
136136
137137
:math:`f'=\dfrac{df}{dt}`
@@ -170,7 +170,7 @@ def time_derivative(data, tfilter=None):
170170
return f
171171

172172
def probability_of_detection(observed, actual, tfilter=None):
173-
"""
173+
r"""
174174
Compute probability of detection (PD) for each column, defined as:
175175
176176
:math:`PD=\dfrac{TP}{TP+FN}`
@@ -228,7 +228,7 @@ def probability_of_detection(observed, actual, tfilter=None):
228228
return PD
229229

230230
def false_alarm_rate(observed, actual, tfilter=None):
231-
"""
231+
r"""
232232
Compute false alarm rate (FAR) for each column, defined as:
233233
234234
:math:`FAR=\dfrac{TN}{TN+FP}`

Diff for: ‎pecos/monitoring.py

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Original file line numberDiff line numberDiff line change
@@ -876,7 +876,7 @@ def check_custom_streaming(self, quality_control_func, window, key=None,
876876
assert isinstance(metadata[t_timestamp], pd.Series), 'metadata returned by quality_control_func must be of type pd.Series'
877877

878878
np_mask[t] = mask_t.values
879-
np_data[~np_mask] = np.NAN
879+
np_data[~np_mask] = np.nan
880880

881881
# rebase
882882
if rebase is not None:

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