Merge pull request #32 from chimaerase/update-pre-commit

Update pre commit and CI configs

.github/workflows/ci_test.yml

@@ -5,7 +5,7 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
-  release: 
+  release:
     types:
       - published
 
@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, '3.10']
 
     steps:
     - name: Checkout repository
@@ -57,10 +57,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: "3.7"
+        python-version: "3.10"
     - name: Install non-python dependencies on linux
       run: |
         sudo apt install libopenmpi-dev
@@ -88,7 +88,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.7'
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -103,4 +103,4 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        twine upload dist/*
+        twine upload dist/*

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
 -   repo: https://github.com/ambv/black
-    rev: 19.10b0
+    rev: 22.10.0
     hooks:
     - id: black
-      args: ["--config=pyproject.toml", "--check"]
+      args: ["--config=pyproject.toml"]
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: "3.7.7"
+    rev: 5.0.4
     hooks:
     - id: flake8
       args: ["--config=.flake8"]
 - repo: https://github.com/timothycrosley/isort
-  rev: 5.6.1
+  rev: 5.10.1
   hooks:
     - id: isort
 

Makefile

@@ -35,11 +35,7 @@ init:
 	@./venv/bin/python3 -m pip install -e .
 
 format:
-	black .
-
-lint:
-	black --check .
-	flake8 .
+	pre-commit run --all-files
 
 clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
 
@@ -61,7 +57,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr htmlcov/
 
-test: lint ## run tests quickly with the default Python
+test: format ## run tests quickly with the default Python
 	pytest -v --durations=10 --full-trace --cov-report html --cov-config .coveragerc --cov=PTMCMCSampler tests
 
 coverage: test ## check code coverage quickly with the default Python
@@ -74,7 +70,7 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 test-sdist: ## Test source distribution
-	mkdir tmp  
+	mkdir tmp
 	cd tmp
 	python -m venv venv-sdist
 	venv-sdist/bin/python -m pip install --upgrade pip setuptools wheel
@@ -83,7 +79,7 @@ test-sdist: ## Test source distribution
 	rm -rf tmp venv-sdist
 
 test-wheel: ## Test wheel
-	mkdir tmp2  
+	mkdir tmp2
 	cd tmp2
 	python -m venv venv-wheel
 	venv-wheel/bin/python -m pip install --upgrade pip setuptools

PTMCMCSampler/PTMCMCSampler.py

@@ -705,7 +705,7 @@ def temperatureLadder(self, Tmin, Tmax=None, tstep=None):
                 tstep = np.exp(np.log(Tmax / Tmin) / (self.nchain - 1))
             ladder = np.zeros(self.nchain)
             for ii in range(self.nchain):
-                ladder[ii] = Tmin * tstep ** ii
+                ladder[ii] = Tmin * tstep**ii
         else:
             ladder = np.array([1])
 

PTMCMCSampler/nutsjump.py

@@ -225,10 +225,10 @@ def __call__(self, x, iter, beta):
         dist = np.random.randn()
 
         # Do the leapfrog
-        mq0 = q0 + 0.5 * vec * self.cd ** 2 * np.dot(vec, grad0) / 2 / val
+        mq0 = q0 + 0.5 * vec * self.cd**2 * np.dot(vec, grad0) / 2 / val
         q1 = mq0 + dist * vec * self.cd / np.sqrt(val)
         logp1, grad1 = self.func_grad_white(q1)
-        mq1 = q1 + 0.5 * vec * self.cd ** 2 * np.dot(vec, grad1) / 2 / val
+        mq1 = q1 + 0.5 * vec * self.cd**2 * np.dot(vec, grad1) / 2 / val
 
         qxy = 0.5 * (np.sum((mq0 - q1) ** 2 / val) - np.sum((mq1 - q0) ** 2 / val))
 
@@ -454,16 +454,16 @@ def find_reasonable_epsilon(self, theta0, grad0, logp0):
 
         a = 2.0 * float((acceptprob > 0.5)) - 1.0
         # Keep moving epsilon in that direction until acceptprob crosses 0.5.
-        while (acceptprob ** a) > (2.0 ** (-a)):
-            epsilon = epsilon * (2.0 ** a)
+        while (acceptprob**a) > (2.0 ** (-a)):
+            epsilon = epsilon * (2.0**a)
             _, rprime, _, logpprime = self.leapfrog(theta0, r0, grad0, epsilon)
 
             acceptprob = np.exp(self.loghamiltonian(logpprime, rprime) - self.loghamiltonian(logp0, r0))
 
         return epsilon
 
     def stop_criterion(self, thetaminus, thetaplus, rminus, rplus, force_trajlen, index):
-        """ Compute the stop condition in the main loop
+        """Compute the stop condition in the main loop
         dot(dtheta, rminus) >= 0 & dot(dtheta, rplus >= 0)
 
         INPUTS
@@ -809,7 +809,7 @@ def __call__(self, x, iter, beta):
             if iter <= self.nburn:
                 # Still in the burn-in phase. So adjust epsilon
                 self.epsilon = np.exp(self.mu - np.sqrt(self.iter) / self.gamma * self.Hbar)
-                eta = self.iter ** -self.kappa
+                eta = self.iter**-self.kappa
                 self.epsilonbar = np.exp((1.0 - eta) * np.log(self.epsilonbar) + eta * np.log(self.epsilon))
 
             else: