Merging from master

.flake8

@@ -3,9 +3,12 @@ max-line-length = 120
 max-complexity = 45
 ignore =
   E203
-  W503      # line break before binary operator; conflicts with black
-  E722      # bare except ok
-  E731      # lambda expressions ok
+  # line break before binary operator; conflicts with black
+  W503
+  # bare except ok      
+  E722
+  # lambda expressions ok      
+  E731      
 exclude =
     .git
     .tox
@@ -14,4 +17,5 @@ exclude =
     dist
     docs
     .enterprise
-    enterprise/src
+    enterprise/src
+    .venv

.github/workflows/ci_test.yml

@@ -21,9 +21,9 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies on mac
@@ -53,7 +53,7 @@ jobs:
     - name: Test with pytest
       run: make test
     - name: Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       #with:
       #  fail_ci_if_error: true
 
@@ -65,9 +65,9 @@ jobs:
     if: github.event_name == 'release'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: "3.7"
     - name: Install non-python dependencies on linux
@@ -111,9 +111,9 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release'
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.7'
     - name: Install dependencies

.gitignore

@@ -71,6 +71,8 @@ target/
 
 # virtual environment
 .enterprise
+# standard-ish virtual environment for VSCode
+.venv
 
 # vscode
 .vscode

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
     - id: black
       args: ["--config=pyproject.toml", "--check"]
--   repo: https://gitlab.com/pycqa/flake8
+-   repo: https://github.com/pycqa/flake8
     rev: "3.7.7"
     hooks:
     - id: flake8

pyproject.toml

@@ -2,7 +2,7 @@
 line-length = 120
 target_version = ['py38']
 include = '\.pyi?$'
-exclude = '''
+extend-exclude = '''
 
 (
   /(

tests/test_gp_coefficients.py

@@ -300,8 +300,8 @@ def test_conditional_gp(self):
 
         # build index for the global coefficient vector
         idx, ntot = {}, 0
-        for l, v in cmean.items():
-            idx[l] = slice(ntot, ntot + len(v))
+        for c_name, v in cmean.items():
+            idx[c_name] = slice(ntot, ntot + len(v))
             ntot = ntot + len(v)
 
         # repeat the computation using the common-signal formalism
@@ -318,8 +318,8 @@ def test_conditional_gp(self):
 
         # check mean values
         msg = "Conditional GP coefficient value does not match"
-        for l, v in cmean.items():
-            assert np.allclose(mn[idx[l]], v, atol=1e-4, rtol=1e-4), msg
+        for c_name, v in cmean.items():
+            assert np.allclose(mn[idx[c_name]], v, atol=1e-4, rtol=1e-4), msg
 
         # check variances
         par = "B1937+21_linear_timing_model_coefficients"
@@ -360,8 +360,8 @@ def test_conditional_gp(self):
         cmean = c.get_mean_coefficients(p0)
 
         idx, ntot = {}, 0
-        for l, v in cmean.items():
-            idx[l] = slice(ntot, ntot + len(v))
+        for c_name, v in cmean.items():
+            idx[c_name] = slice(ntot, ntot + len(v))
             ntot = ntot + len(v)
 
         TNrs = pta.get_TNr(p0)
@@ -375,8 +375,8 @@ def test_conditional_gp(self):
         mn = ch(TNr)
 
         msg = "Conditional GP coefficient value does not match for common GP"
-        for l, v in cmean.items():
-            assert np.allclose(mn[idx[l]], v)
+        for c_name, v in cmean.items():
+            assert np.allclose(mn[idx[c_name]], v)
 
 
 class TestGPCoefficientsPint(TestGPCoefficients):