From 89d3fe7e78697d80a00325bfaa2929c9cddf571e Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 11:44:26 -0500
Subject: [PATCH 01/31] Updating github actions

---
 .github/workflows/ci_test.yml | 80 ++++++++++++++++++++++++++---------
 Makefile                      |  6 +--
 pyproject.toml                | 12 ++++--
 requirements.txt              |  8 ++--
 setup.py                      |  9 +++-
 tests/test_pulsar.py          |  8 ++++
 6 files changed, 90 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 1afa64b7..3616142c 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -1,51 +1,89 @@
-name: CI-Tests
+name: enterprise CI targets
 
 on:
   push:
-#    branches:
-#    - master
+    branches: [ master ]
   pull_request:
+    branches: [ master ]
+  release: 
+    types:
+      - published
+
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
-  build:
+  test-linux:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: [3.6, 3.7, 3.8]
+
     steps:
-    - name: Checkout Repository
+    - name: Checkout repository
       uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Pre-install
+    - name: Install non-python dependencies
       run: |
         sudo apt-get install libsuitesparse-dev
-        python -m pip install --upgrade pip
-    - name: Install Dependencies
+        curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
+    - name: Install dependencies and package
       run: |
-        cat requirements_dev.txt | xargs -n 1 -L 1 pip install
-        cat requirements.txt | xargs -n 1 -L 1 pip install
-        python setup.py install
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest black pytest-cov
+        pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
         pip freeze
-    - name: Run Tests and Lint
-      run: |
-        pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
-        make lint
+    - name: Run lint
+      run: make lint
+    - name: Test with pytest
+      run: pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
     - name: Codecov
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: true
+
+
+  test-mac:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install non-python dependencies
+      run: |
+        brew install suite-sparse
+        curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
+    - name: Install dependencies and package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest black pytest-cov
+        pip install -e .
+    - name: Display Python, pip, setuptools, and all installed versions
+      run: |
+        python -c "import sys; print(f'Python {sys.version}')"
+        python -c "import pip; print(f'pip {pip.__version__}')"
+        python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
+        pip freeze
+    - name: Run lint
+      run: make lint
+    - name: Test with pytest
+      run: pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
+    - name: Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: true
\ No newline at end of file
diff --git a/Makefile b/Makefile
index e15585cf..375b358a 100644
--- a/Makefile
+++ b/Makefile
@@ -28,10 +28,10 @@ help:
 
 init:
 	@python3 -m venv .enterprise --prompt enterprise
-	@./.enterprise/bin/python3 -m pip install numpy
+	@./.enterprise/bin/python3 -m pip install -U pip
+	@./.enterprise/bin/python3 -m pip install numpy cython
 	@./.enterprise/bin/python3 -m pip install -r requirements.txt -U
 	@./.enterprise/bin/python3 -m pip install -r requirements_dev.txt -U
-	@./.enterprise/bin/python3 -m pip install libstempo --install-option="--with-tempo2=$(TEMPO2)"
 	@./.enterprise/bin/python3 -m pre_commit install --install-hooks --overwrite
 	@./.enterprise/bin/python3 -m pip install -e .
 
@@ -62,7 +62,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr htmlcov/
 
-test: ## run tests quickly with the default Python
+test: lint ## run tests quickly with the default Python
 	pytest -v --full-trace --cov-config .coveragerc --cov=enterprise tests
 
 #test-all: ## run tests on every Python version with tox
diff --git a/pyproject.toml b/pyproject.toml
index 571df8af..8d16d98a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,13 @@ exclude = '''
     | .enterprise
     | enterprise/src
   )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
 )
-'''
\ No newline at end of file
+'''
+[build-system]
+requires = [
+    "setuptools>=40.8.0",
+    "wheel",
+    "Cython>=0.22", # need for scikit-sparse
+    "numpy>=1.15.0" # need for scikit-sparse
+]
+build-backend = "setuptools.build_meta"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 35be0917..66a6495e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,8 @@
 numpy>=1.16.3
 scipy>=1.2.0
 ephem>=3.7.6.0
-Cython>=0.28.5
 jplephem==2.6
-setuptools>=40.0.0
 healpy>=1.14.0
-scikit-sparse>=0.4.2 --no-binary scikit-sparse
-git+https://github.com/nanograv/PINT.git@master#egg=pint-pulsar
-git+https://github.com/vallis/libstempo.git@master#egg=libstempo --install-option="--force-tempo2-install"
+scikit-sparse>=0.4.2
+pint-pulsar>=0.8.2
+git+https://github.com/jellis18/libstempo.git@master#egg=libstempo
diff --git a/setup.py b/setup.py
index f1575ce0..de3b3667 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,14 @@
     history = history_file.read()
 
 requirements = [
-    # TODO: put package requirements here
+    "numpy>=1.16.3",
+    "scipy>=1.2.0",
+    "ephem>=3.7.6.0",
+    "jplephem==2.6",
+    "healpy>=1.14.0",
+    "scikit-sparse>=0.4.2",
+    "pint-pulsar>=0.8.2",
+    "libstempo @ git+https://github.com/jellis18/libstempo.git@master#egg=libstempo",
 ]
 
 test_requirements = []
diff --git a/tests/test_pulsar.py b/tests/test_pulsar.py
index 95cad51e..41fb6901 100644
--- a/tests/test_pulsar.py
+++ b/tests/test_pulsar.py
@@ -10,6 +10,8 @@
 """
 
 
+import os
+import shutil
 import unittest
 
 import numpy as np
@@ -31,6 +33,10 @@ def setUpClass(cls):
         # initialize Pulsar class
         cls.psr = Pulsar(datadir + "/B1855+09_NANOGrav_9yv1.gls.par", datadir + "/B1855+09_NANOGrav_9yv1.tim")
 
+    @classmethod
+    def tearDownClass(cls):
+        shutil.rmtree("pickle_dir")
+
     def test_residuals(self):
         """Check Residual shape."""
 
@@ -117,6 +123,8 @@ def test_to_pickle(self):
         with open("B1855+09.pkl", "rb") as f:
             pkl_psr = pickle.load(f)
 
+        os.remove("B1855+09.pkl")
+
         assert np.allclose(self.psr.residuals, pkl_psr.residuals, rtol=1e-10)
 
         self.psr.to_pickle("pickle_dir")

From 213563303e67d4496abe2a41a493b7449c63b628 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 11:52:32 -0500
Subject: [PATCH 02/31] Update CI

---
 .github/workflows/ci_test.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 3616142c..a92ade95 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -31,15 +31,15 @@ jobs:
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools wheel
         python -m pip install flake8 pytest black pytest-cov
-        pip install -e .
+        python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-        pip freeze
+        python -m pip freeze
     - name: Run lint
       run: make lint
     - name: Test with pytest
@@ -70,15 +70,15 @@ jobs:
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools wheel
         python -m pip install flake8 pytest black pytest-cov
-        pip install -e .
+        python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-        pip freeze
+        python -m pip freeze
     - name: Run lint
       run: make lint
     - name: Test with pytest

From 645e3503ea323f25b11c2688504fe2dc261f212c Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 12:21:32 -0500
Subject: [PATCH 03/31] add numpy cython install

---
 .github/workflows/ci_test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index a92ade95..2be092b6 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -33,6 +33,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install flake8 pytest black pytest-cov
+        python -m pip install numpy cython
         python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
@@ -72,6 +73,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install flake8 pytest black pytest-cov
+        python -m pip install numpy cython
         python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |

From b52dada23da5355021b2e0b41e45d3e32c51670f Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 12:54:14 -0500
Subject: [PATCH 04/31] Check brew list

---
 .github/workflows/ci_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 2be092b6..1c6bea77 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,6 +67,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
+        brew list
         brew install suite-sparse
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package

From 264ac0fc2dd036ef11ade0fa05d0549698e3d8e4 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 13:27:13 -0500
Subject: [PATCH 05/31] Automake

---
 .github/workflows/ci_test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 1c6bea77..5285bca9 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,8 +67,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
-        brew list
-        brew install suite-sparse
+        brew install suite-sparse automake
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From 786b6bdfc93983c5e03cc2b306dda74d5b0b971a Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 17:05:56 -0500
Subject: [PATCH 06/31] gfortran

---
 .github/workflows/ci_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 5285bca9..5c3556d0 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,7 +67,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
-        brew install suite-sparse automake
+        brew install suite-sparse automake gfortran
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From 01ad5093ad2bedf483e3b068942260209d58f8e9 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 18:09:38 -0500
Subject: [PATCH 07/31] alias

---
 .github/workflows/ci_test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 5c3556d0..0188425f 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,7 +67,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
-        brew install suite-sparse automake gfortran
+        alias gfortran=gfortran-9
+        brew install suite-sparse automake
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From 2d5d4110b1cb7a785235e4441ab581af3e2ae084 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 18:19:56 -0500
Subject: [PATCH 08/31] environment variable

---
 .github/workflows/ci_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 0188425f..0d23fb89 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,8 +67,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
-        alias gfortran=gfortran-9
         brew install suite-sparse automake
+        export FC=gfortran-10
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From 819625ec85dea5468072d755554278522b1ec946 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 18:43:54 -0500
Subject: [PATCH 09/31] brew link

---
 .github/workflows/ci_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 0d23fb89..22896d37 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,8 +67,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
+        brew link gfortran
         brew install suite-sparse automake
-        export FC=gfortran-10
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From 1fe00fa14dc1b7d465504eb59027c6a4e0419592 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 7 Mar 2021 20:33:10 -0500
Subject: [PATCH 10/31] try again

---
 .github/workflows/ci_test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 22896d37..6515d416 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -67,7 +67,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies
       run: |
-        brew link gfortran
+        brew unlink gcc && brew link gcc
+        which gfortran
         brew install suite-sparse automake
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package

From cbc877d50bccfd4fbe5c2ff6e2dbc6a5318e7413 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Mon, 8 Mar 2021 07:39:27 -0500
Subject: [PATCH 11/31] one block

---
 .github/workflows/ci_test.yml | 54 +++++++----------------------------
 1 file changed, 10 insertions(+), 44 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 6515d416..ab5afa41 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -11,11 +11,12 @@ on:
 
 
 jobs:
-  test-linux:
-    runs-on: ubuntu-latest
+  tests:
+    runs-on: ${{ os.matrix.os }}
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8]
 
     steps:
@@ -25,51 +26,16 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install non-python dependencies
+      - name: Install non-python dependencies on mac
+      if: runner.os == 'macOS'
       run: |
-        sudo apt-get install libsuitesparse-dev
+        brew unlink gcc && brew link gcc
+        brew install automake suite-sparse
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
-    - name: Install dependencies and package
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install flake8 pytest black pytest-cov
-        python -m pip install numpy cython
-        python -m pip install -e .
-    - name: Display Python, pip, setuptools, and all installed versions
+    - name: Install non-python dependencies on linux
+      if: runner.os == 'Linux'
       run: |
-        python -c "import sys; print(f'Python {sys.version}')"
-        python -c "import pip; print(f'pip {pip.__version__}')"
-        python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-        python -m pip freeze
-    - name: Run lint
-      run: make lint
-    - name: Test with pytest
-      run: pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
-    - name: Codecov
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: true
-
-
-  test-mac:
-    runs-on: macos-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [3.6, 3.7, 3.8]
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install non-python dependencies
-      run: |
-        brew unlink gcc && brew link gcc
-        which gfortran
-        brew install suite-sparse automake
+        sudo apt-get install libsuitesparse-dev
         curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |

From c5a2962f21579dc10684907f73e6d8be25fa4850 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Mon, 8 Mar 2021 07:40:39 -0500
Subject: [PATCH 12/31] fix typo

---
 .github/workflows/ci_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index ab5afa41..230acfe2 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -12,7 +12,7 @@ on:
 
 jobs:
   tests:
-    runs-on: ${{ os.matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:

From c0c639b173e79ed6dc22aca4b541efc4d7085513 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Mon, 8 Mar 2021 07:42:07 -0500
Subject: [PATCH 13/31] indent

---
 .github/workflows/ci_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 230acfe2..e5cbfdc2 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -26,7 +26,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-      - name: Install non-python dependencies on mac
+    - name: Install non-python dependencies on mac
       if: runner.os == 'macOS'
       run: |
         brew unlink gcc && brew link gcc

From 0ef8c1e6c6c0fd0a022437af3bec43fa94a93bc7 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Mon, 8 Mar 2021 17:21:11 -0500
Subject: [PATCH 14/31] remove numpy and cython from pyproject

---
 pyproject.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8d16d98a..6dcc2e86 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,5 @@ exclude = '''
 requires = [
     "setuptools>=40.8.0",
     "wheel",
-    "Cython>=0.22", # need for scikit-sparse
-    "numpy>=1.15.0" # need for scikit-sparse
 ]
 build-backend = "setuptools.build_meta"
\ No newline at end of file

From c76dcf1d8e9d6920ebbc91a87130b17b90b4f6a5 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 08:29:52 -0500
Subject: [PATCH 15/31] change jellis-> vallis and add python requirement

---
 .github/workflows/ci_test.yml | 4 ++--
 requirements.txt              | 2 +-
 setup.py                      | 3 ++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index e5cbfdc2..4871b797 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -31,12 +31,12 @@ jobs:
       run: |
         brew unlink gcc && brew link gcc
         brew install automake suite-sparse
-        curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
     - name: Install non-python dependencies on linux
       if: runner.os == 'Linux'
       run: |
         sudo apt-get install libsuitesparse-dev
-        curl -sSL https://raw.githubusercontent.com/jellis18/libstempo/master/install_tempo2.sh | sh
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
     - name: Install dependencies and package
       run: |
         python -m pip install --upgrade pip setuptools wheel
diff --git a/requirements.txt b/requirements.txt
index 66a6495e..0c6605b6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,4 +5,4 @@ jplephem==2.6
 healpy>=1.14.0
 scikit-sparse>=0.4.2
 pint-pulsar>=0.8.2
-git+https://github.com/jellis18/libstempo.git@master#egg=libstempo
+git+https://github.com/vallis/libstempo.git@master#egg=libstempo
diff --git a/setup.py b/setup.py
index de3b3667..54e380a0 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
     "healpy>=1.14.0",
     "scikit-sparse>=0.4.2",
     "pint-pulsar>=0.8.2",
-    "libstempo @ git+https://github.com/jellis18/libstempo.git@master#egg=libstempo",
+    "libstempo @ git+https://github.com/vallis/libstempo.git@master#egg=libstempo",
 ]
 
 test_requirements = []
@@ -35,6 +35,7 @@
     package_dir={"enterprise": "enterprise"},
     include_package_data=True,
     package_data={"enterprise": ["datafiles/*", "datafiles/ephemeris/*", "datafiles/ng9/*", "datafiles/mdc_open1/*"]},
+    python_requires=">=3.6, <3.9",
     install_requires=requirements,
     license="MIT license",
     zip_safe=False,

From 76a5f7f08a5a50196089f83220a54bf62effbb42 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 09:09:36 -0500
Subject: [PATCH 16/31] Using logger and adding isort

---
 .pre-commit-config.yaml              |  5 +++++
 Makefile                             |  2 +-
 enterprise/pulsar.py                 | 17 ++++++++---------
 enterprise/signals/selections.py     |  1 -
 enterprise/signals/signal_base.py    | 16 ++++++++--------
 enterprise/signals/utils.py          | 15 ++++++++-------
 enterprise/signals/white_signals.py  |  1 -
 tests/test_hierarchical_parameter.py |  1 -
 tests/test_vector_parameter.py       |  1 -
 9 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6208b137..b200a92b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,3 +9,8 @@ repos:
     hooks:
     - id: flake8
       args: ["--config=.flake8"]
+- repo: https://github.com/timothycrosley/isort
+  rev: 5.6.1
+  hooks:
+    - id: isort
+
diff --git a/Makefile b/Makefile
index 375b358a..d3d3f8ae 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ help:
 
 init:
 	@python3 -m venv .enterprise --prompt enterprise
-	@./.enterprise/bin/python3 -m pip install -U pip
+	@./.enterprise/bin/python3 -m pip install -U pip setuptools wheel
 	@./.enterprise/bin/python3 -m pip install numpy cython
 	@./.enterprise/bin/python3 -m pip install -r requirements.txt -U
 	@./.enterprise/bin/python3 -m pip install -r requirements_dev.txt -U
diff --git a/enterprise/pulsar.py b/enterprise/pulsar.py
index f9f5ba2e..2de0a944 100644
--- a/enterprise/pulsar.py
+++ b/enterprise/pulsar.py
@@ -6,8 +6,8 @@
 import logging
 import os
 
-import astropy.units as u
 import astropy.constants as const
+import astropy.units as u
 import numpy as np
 from ephem import Ecliptic, Equatorial
 
@@ -19,19 +19,21 @@
 except:
     import pickle
 
+logger = logging.getLogger(__name__)
+
 try:
     import libstempo as t2
 except ImportError:
-    print("Ooh, no libstempo?")
+    logger.warning("libstempo not installed. Will use PINT instead.")
     t2 = None
 
 try:
     import pint
-    from pint.toa import TOAs
-    from pint.models import get_model_and_toas, TimingModel
+    from pint.models import TimingModel, get_model_and_toas
     from pint.residuals import Residuals as resids
+    from pint.toa import TOAs
 except ImportError:
-    print("Cannot import PINT? Meh...")
+    logger.warning("PINT not installed. Will use libstempo instead.")
     pint = None
 
 
@@ -39,9 +41,6 @@
     err_msg = "Must have either PINT or libstempo timing package installed"
     raise ImportError(err_msg)
 
-# logging.basicConfig(format="%(levelname)s: %(name)s: %(message)s", level=logging.INFO)
-logger = logging.getLogger(__name__)
-
 
 def get_maxobs(timfile):
     """Utility function to return number of lines in tim file.
@@ -575,4 +574,4 @@ def Pulsar(*args, **kwargs):
             os.chdir(cwd)
             return Tempo2Pulsar(t2pulsar, sort=sort, drop_t2pulsar=drop_t2pulsar, planets=planets)
     else:
-        print("Unknown arguments {}".format(args))
+        logger.error("Unknown arguments {}".format(args))
diff --git a/enterprise/signals/selections.py b/enterprise/signals/selections.py
index f7de81d0..daeac4e9 100644
--- a/enterprise/signals/selections.py
+++ b/enterprise/signals/selections.py
@@ -2,7 +2,6 @@
 """Contains various selection functions to mask parameters by backend flags,
 time-intervals, etc."""
 
-from __future__ import absolute_import, division, print_function, unicode_literals
 
 import functools
 import inspect
diff --git a/enterprise/signals/signal_base.py b/enterprise/signals/signal_base.py
index f4e3c07f..cb0cc787 100644
--- a/enterprise/signals/signal_base.py
+++ b/enterprise/signals/signal_base.py
@@ -3,14 +3,13 @@
 Defines the signal base classes and metaclasses. All signals will then be
 derived from these base classes.
 """
-from __future__ import absolute_import, division, print_function, unicode_literals
-
 import collections
 
 try:
     from collections.abc import Sequence
 except:
     from collections import Sequence
+
 import itertools
 import logging
 
@@ -546,10 +545,11 @@ def _setpulsarcliques(self, slices, phis):
                         try:
                             self._cliques[slices[sc].start + phiind] = self._clcount
                             self._clcount = self._clcount + 1
-                        except:
-                            print(self._cliques.shape)
-                            print("phiind", phiind, len(phiind))
-                            print(slices)
+                        except Exception:
+                            logger.exception("Exception raised in computing cliques")
+                            logger.info(self._cliques.shape)
+                            logger.info("phiind", phiind, len(phiind))
+                            logger.info(slices)
                             raise
 
     def get_phi(self, params, cliques=False):
@@ -654,7 +654,7 @@ def summary(self, include_params=True, to_stdout=False):
         :param include_params: [bool]
             list all parameters for each signal
         :param to_stdout: [bool]
-            print summary to `stdout` instead of returning it
+            logger.info summary to `stdout` instead of returning it
         :return: [string]
         """
         summary = ""
@@ -684,7 +684,7 @@ def summary(self, include_params=True, to_stdout=False):
         summary += "Fixed params: {}\n".format(copcount)
         summary += "Number of pulsars: {}\n".format(len(self._signalcollections))
         if to_stdout:
-            print(summary)
+            logger.info(summary)
         else:
             return summary
 
diff --git a/enterprise/signals/utils.py b/enterprise/signals/utils.py
index fe1f1ccc..e90ea0cd 100644
--- a/enterprise/signals/utils.py
+++ b/enterprise/signals/utils.py
@@ -4,7 +4,7 @@
 functions for use in other modules.
 """
 
-from __future__ import absolute_import, division, print_function, unicode_literals
+import logging
 
 import numpy as np
 import scipy.linalg as sl
@@ -16,22 +16,23 @@
 
 import enterprise
 from enterprise import constants as const
-from enterprise.signals.parameter import function
-from enterprise.signals.gp_priors import powerlaw, turnover  # noqa: F401
 from enterprise import signals as sigs  # noqa: F401
 from enterprise.signals.gp_bases import (  # noqa: F401
-    createfourierdesignmatrix_red,
     createfourierdesignmatrix_dm,
     createfourierdesignmatrix_env,
-    createfourierdesignmatrix_ephem,
     createfourierdesignmatrix_eph,
+    createfourierdesignmatrix_ephem,
+    createfourierdesignmatrix_red,
 )
+from enterprise.signals.gp_priors import powerlaw, turnover  # noqa: F401
+from enterprise.signals.parameter import function
 
+logger = logging.getLogger(__name__)
 
 try:
     from sksparse.cholmod import cholesky
-except:
-    print("You'll need sksparse for get_coefficients() with common signals!")
+except ImportError:
+    logger.warning("sksparse not installed. You'll need sksparse for get_coefficients() with common signals!")
 
 
 def get_coefficients(pta, params, n=1, phiinv_method="cliques", common_sparse=False):
diff --git a/enterprise/signals/white_signals.py b/enterprise/signals/white_signals.py
index d6703c1d..95b78871 100644
--- a/enterprise/signals/white_signals.py
+++ b/enterprise/signals/white_signals.py
@@ -3,7 +3,6 @@
 defined as the class of signals that only modifies the white noise matrix `N`.
 """
 
-from __future__ import absolute_import, division, print_function, unicode_literals
 
 import numpy as np
 import scipy.sparse
diff --git a/tests/test_hierarchical_parameter.py b/tests/test_hierarchical_parameter.py
index b84f7bc7..9e767a0c 100644
--- a/tests/test_hierarchical_parameter.py
+++ b/tests/test_hierarchical_parameter.py
@@ -8,7 +8,6 @@
 Tests for hierarchical parameter functionality
 """
 
-from __future__ import division
 
 import unittest
 
diff --git a/tests/test_vector_parameter.py b/tests/test_vector_parameter.py
index 77ae9faf..3d4b31d6 100644
--- a/tests/test_vector_parameter.py
+++ b/tests/test_vector_parameter.py
@@ -8,7 +8,6 @@
 Tests for vector parameter functionality
 """
 
-from __future__ import division
 
 import unittest
 

From 72fbfe40b55de72127b39e38fe8bf4046d4918f1 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 09:09:57 -0500
Subject: [PATCH 17/31] isort config

---
 .isort.cfg | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 .isort.cfg

diff --git a/.isort.cfg b/.isort.cfg
new file mode 100644
index 00000000..b52cc737
--- /dev/null
+++ b/.isort.cfg
@@ -0,0 +1,6 @@
+[settings]
+include_trailing_comma=True
+indent='    '
+dedup_headings=True
+line_length=120
+multi_line_output=3
\ No newline at end of file

From 6f8926c0801b361e02738a73f8f82f3f528013b2 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 09:12:39 -0500
Subject: [PATCH 18/31] logger.info -> print in docsting

---
 enterprise/signals/signal_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/enterprise/signals/signal_base.py b/enterprise/signals/signal_base.py
index cb0cc787..3cc1cc2c 100644
--- a/enterprise/signals/signal_base.py
+++ b/enterprise/signals/signal_base.py
@@ -654,7 +654,7 @@ def summary(self, include_params=True, to_stdout=False):
         :param include_params: [bool]
             list all parameters for each signal
         :param to_stdout: [bool]
-            logger.info summary to `stdout` instead of returning it
+            print summary to `stdout` instead of returning it
         :return: [string]
         """
         summary = ""

From 2b36b1e52e40e50034ed22d12103269a87fcad86 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 11:14:07 -0500
Subject: [PATCH 19/31] Adding wheels and pypi

---
 .github/workflows/ci_test.yml | 74 ++++++++++++++++++++++++++++++++++-
 Makefile                      |  2 +-
 2 files changed, 74 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 4871b797..4f8a57b0 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -56,4 +56,76 @@ jobs:
     - name: Codecov
       uses: codecov/codecov-action@v1
       with:
-        fail_ci_if_error: true
\ No newline at end of file
+        fail_ci_if_error: true
+
+
+  build:
+    needs: [tests]
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+    - name: Install non-python dependencies on linux
+      run: |
+        sudo apt-get install libsuitesparse-dev
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -r requirements.txt
+        make dist
+    - name: Test the sdist
+      run: |
+        mkdir tmp  
+        cd tmp
+        python -m venv venv-sdist
+        venv-sdist/bin/python -m pip install --upgrade pip setuptools wheel
+        venv-sdist/bin/python -m pip install numpy cython
+        venv-sdist/bin/python -m pip install ../dist/enterprise*.tar.gz
+        venv-sdist/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - name: Test the wheel
+      run: |
+        mkdir tmp2  
+        cd tmp2
+        python -m venv venv-wheel
+        venv-wheel/bin/python -m pip install --upgrade pip setuptools
+        venv-wheel/bin/python -m pip install numpy cython
+        venv-wheel/bin/python -m pip install ../dist/enterprise*.whl
+        venv-wheel/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist/*
+
+
+  deploy:
+    needs: [tests, build]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Download wheel/dist from build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+        path: dist
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        twine upload dist/*
\ No newline at end of file
diff --git a/Makefile b/Makefile
index d3d3f8ae..43a59b17 100644
--- a/Makefile
+++ b/Makefile
@@ -63,7 +63,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 
 test: lint ## run tests quickly with the default Python
-	pytest -v --full-trace --cov-config .coveragerc --cov=enterprise tests
+	pytest -v --durations=10 --full-trace --cov-config .coveragerc --cov=enterprise tests
 
 #test-all: ## run tests on every Python version with tox
 #	tox

From 7bf63850e01516623022a92bbc365f1a19e1cd1d Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 15:18:37 -0500
Subject: [PATCH 20/31] Adding "build requirements" for scikit-sparse

---
 .github/workflows/ci_test.yml | 1 +
 enterprise/pulsar.py          | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 4f8a57b0..7fb1b01c 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -78,6 +78,7 @@ jobs:
     - name: Build
       run: |
         python -m pip install --upgrade pip setuptools wheel
+        pip install numpy==1.16.3 cython
         pip install -r requirements.txt
         make dist
     - name: Test the sdist
diff --git a/enterprise/pulsar.py b/enterprise/pulsar.py
index 2de0a944..88bd7e9e 100644
--- a/enterprise/pulsar.py
+++ b/enterprise/pulsar.py
@@ -118,7 +118,7 @@ def sort_data(self):
         """Sort data by time."""
         if self._sort:
             self._isort = np.argsort(self._toas, kind="mergesort")
-            self._iisort = np.zeros(len(self._isort), dtype=np.int)
+            self._iisort = np.zeros(len(self._isort), dtype=int)
             for ii, p in enumerate(self._isort):
                 self._iisort[p] = ii
         else:

From 8da5573add417ed9df157c7ac5f3332ded8f4de6 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sat, 13 Mar 2021 18:05:36 -0500
Subject: [PATCH 21/31] Updating github actions and requirements (#3)

* Updating github actions

* Update CI

* add numpy cython install

* Check brew list

* Automake

* gfortran

* alias

* environment variable

* brew link

* try again

* one block

* fix typo

* indent

* remove numpy and cython from pyproject

* change jellis-> vallis and add python requirement

* Using logger and adding isort

* isort config

* logger.info -> print in docsting

* Adding wheels and pypi

* Adding "build requirements" for scikit-sparse
---
 .github/workflows/ci_test.yml        | 127 ++++++++++++++++++++++-----
 .isort.cfg                           |   6 ++
 .pre-commit-config.yaml              |   5 ++
 Makefile                             |   8 +-
 enterprise/pulsar.py                 |  19 ++--
 enterprise/signals/selections.py     |   1 -
 enterprise/signals/signal_base.py    |  14 +--
 enterprise/signals/utils.py          |  15 ++--
 enterprise/signals/white_signals.py  |   1 -
 pyproject.toml                       |  10 ++-
 requirements.txt                     |   8 +-
 setup.py                             |  10 ++-
 tests/test_hierarchical_parameter.py |   1 -
 tests/test_pulsar.py                 |   8 ++
 tests/test_vector_parameter.py       |   1 -
 15 files changed, 170 insertions(+), 64 deletions(-)
 create mode 100644 .isort.cfg

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 1afa64b7..7fb1b01c 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -1,51 +1,132 @@
-name: CI-Tests
+name: enterprise CI targets
 
 on:
   push:
-#    branches:
-#    - master
+    branches: [ master ]
   pull_request:
+    branches: [ master ]
+  release: 
+    types:
+      - published
+
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
-  build:
-    runs-on: ubuntu-latest
+  tests:
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8]
+
     steps:
-    - name: Checkout Repository
+    - name: Checkout repository
       uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Pre-install
+    - name: Install non-python dependencies on mac
+      if: runner.os == 'macOS'
+      run: |
+        brew unlink gcc && brew link gcc
+        brew install automake suite-sparse
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Install non-python dependencies on linux
+      if: runner.os == 'Linux'
       run: |
         sudo apt-get install libsuitesparse-dev
-        python -m pip install --upgrade pip
-    - name: Install Dependencies
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Install dependencies and package
       run: |
-        cat requirements_dev.txt | xargs -n 1 -L 1 pip install
-        cat requirements.txt | xargs -n 1 -L 1 pip install
-        python setup.py install
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install flake8 pytest black pytest-cov
+        python -m pip install numpy cython
+        python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-        pip freeze
-    - name: Run Tests and Lint
-      run: |
-        pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
-        make lint
+        python -m pip freeze
+    - name: Run lint
+      run: make lint
+    - name: Test with pytest
+      run: pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
     - name: Codecov
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: true
+
+
+  build:
+    needs: [tests]
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+    - name: Install non-python dependencies on linux
+      run: |
+        sudo apt-get install libsuitesparse-dev
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install numpy==1.16.3 cython
+        pip install -r requirements.txt
+        make dist
+    - name: Test the sdist
+      run: |
+        mkdir tmp  
+        cd tmp
+        python -m venv venv-sdist
+        venv-sdist/bin/python -m pip install --upgrade pip setuptools wheel
+        venv-sdist/bin/python -m pip install numpy cython
+        venv-sdist/bin/python -m pip install ../dist/enterprise*.tar.gz
+        venv-sdist/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - name: Test the wheel
+      run: |
+        mkdir tmp2  
+        cd tmp2
+        python -m venv venv-wheel
+        venv-wheel/bin/python -m pip install --upgrade pip setuptools
+        venv-wheel/bin/python -m pip install numpy cython
+        venv-wheel/bin/python -m pip install ../dist/enterprise*.whl
+        venv-wheel/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist/*
+
+
+  deploy:
+    needs: [tests, build]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Download wheel/dist from build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+        path: dist
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        twine upload dist/*
\ No newline at end of file
diff --git a/.isort.cfg b/.isort.cfg
new file mode 100644
index 00000000..b52cc737
--- /dev/null
+++ b/.isort.cfg
@@ -0,0 +1,6 @@
+[settings]
+include_trailing_comma=True
+indent='    '
+dedup_headings=True
+line_length=120
+multi_line_output=3
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6208b137..b200a92b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,3 +9,8 @@ repos:
     hooks:
     - id: flake8
       args: ["--config=.flake8"]
+- repo: https://github.com/timothycrosley/isort
+  rev: 5.6.1
+  hooks:
+    - id: isort
+
diff --git a/Makefile b/Makefile
index e15585cf..43a59b17 100644
--- a/Makefile
+++ b/Makefile
@@ -28,10 +28,10 @@ help:
 
 init:
 	@python3 -m venv .enterprise --prompt enterprise
-	@./.enterprise/bin/python3 -m pip install numpy
+	@./.enterprise/bin/python3 -m pip install -U pip setuptools wheel
+	@./.enterprise/bin/python3 -m pip install numpy cython
 	@./.enterprise/bin/python3 -m pip install -r requirements.txt -U
 	@./.enterprise/bin/python3 -m pip install -r requirements_dev.txt -U
-	@./.enterprise/bin/python3 -m pip install libstempo --install-option="--with-tempo2=$(TEMPO2)"
 	@./.enterprise/bin/python3 -m pre_commit install --install-hooks --overwrite
 	@./.enterprise/bin/python3 -m pip install -e .
 
@@ -62,8 +62,8 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr htmlcov/
 
-test: ## run tests quickly with the default Python
-	pytest -v --full-trace --cov-config .coveragerc --cov=enterprise tests
+test: lint ## run tests quickly with the default Python
+	pytest -v --durations=10 --full-trace --cov-config .coveragerc --cov=enterprise tests
 
 #test-all: ## run tests on every Python version with tox
 #	tox
diff --git a/enterprise/pulsar.py b/enterprise/pulsar.py
index f9f5ba2e..88bd7e9e 100644
--- a/enterprise/pulsar.py
+++ b/enterprise/pulsar.py
@@ -6,8 +6,8 @@
 import logging
 import os
 
-import astropy.units as u
 import astropy.constants as const
+import astropy.units as u
 import numpy as np
 from ephem import Ecliptic, Equatorial
 
@@ -19,19 +19,21 @@
 except:
     import pickle
 
+logger = logging.getLogger(__name__)
+
 try:
     import libstempo as t2
 except ImportError:
-    print("Ooh, no libstempo?")
+    logger.warning("libstempo not installed. Will use PINT instead.")
     t2 = None
 
 try:
     import pint
-    from pint.toa import TOAs
-    from pint.models import get_model_and_toas, TimingModel
+    from pint.models import TimingModel, get_model_and_toas
     from pint.residuals import Residuals as resids
+    from pint.toa import TOAs
 except ImportError:
-    print("Cannot import PINT? Meh...")
+    logger.warning("PINT not installed. Will use libstempo instead.")
     pint = None
 
 
@@ -39,9 +41,6 @@
     err_msg = "Must have either PINT or libstempo timing package installed"
     raise ImportError(err_msg)
 
-# logging.basicConfig(format="%(levelname)s: %(name)s: %(message)s", level=logging.INFO)
-logger = logging.getLogger(__name__)
-
 
 def get_maxobs(timfile):
     """Utility function to return number of lines in tim file.
@@ -119,7 +118,7 @@ def sort_data(self):
         """Sort data by time."""
         if self._sort:
             self._isort = np.argsort(self._toas, kind="mergesort")
-            self._iisort = np.zeros(len(self._isort), dtype=np.int)
+            self._iisort = np.zeros(len(self._isort), dtype=int)
             for ii, p in enumerate(self._isort):
                 self._iisort[p] = ii
         else:
@@ -575,4 +574,4 @@ def Pulsar(*args, **kwargs):
             os.chdir(cwd)
             return Tempo2Pulsar(t2pulsar, sort=sort, drop_t2pulsar=drop_t2pulsar, planets=planets)
     else:
-        print("Unknown arguments {}".format(args))
+        logger.error("Unknown arguments {}".format(args))
diff --git a/enterprise/signals/selections.py b/enterprise/signals/selections.py
index f7de81d0..daeac4e9 100644
--- a/enterprise/signals/selections.py
+++ b/enterprise/signals/selections.py
@@ -2,7 +2,6 @@
 """Contains various selection functions to mask parameters by backend flags,
 time-intervals, etc."""
 
-from __future__ import absolute_import, division, print_function, unicode_literals
 
 import functools
 import inspect
diff --git a/enterprise/signals/signal_base.py b/enterprise/signals/signal_base.py
index f4e3c07f..3cc1cc2c 100644
--- a/enterprise/signals/signal_base.py
+++ b/enterprise/signals/signal_base.py
@@ -3,14 +3,13 @@
 Defines the signal base classes and metaclasses. All signals will then be
 derived from these base classes.
 """
-from __future__ import absolute_import, division, print_function, unicode_literals
-
 import collections
 
 try:
     from collections.abc import Sequence
 except:
     from collections import Sequence
+
 import itertools
 import logging
 
@@ -546,10 +545,11 @@ def _setpulsarcliques(self, slices, phis):
                         try:
                             self._cliques[slices[sc].start + phiind] = self._clcount
                             self._clcount = self._clcount + 1
-                        except:
-                            print(self._cliques.shape)
-                            print("phiind", phiind, len(phiind))
-                            print(slices)
+                        except Exception:
+                            logger.exception("Exception raised in computing cliques")
+                            logger.info(self._cliques.shape)
+                            logger.info("phiind", phiind, len(phiind))
+                            logger.info(slices)
                             raise
 
     def get_phi(self, params, cliques=False):
@@ -684,7 +684,7 @@ def summary(self, include_params=True, to_stdout=False):
         summary += "Fixed params: {}\n".format(copcount)
         summary += "Number of pulsars: {}\n".format(len(self._signalcollections))
         if to_stdout:
-            print(summary)
+            logger.info(summary)
         else:
             return summary
 
diff --git a/enterprise/signals/utils.py b/enterprise/signals/utils.py
index fe1f1ccc..e90ea0cd 100644
--- a/enterprise/signals/utils.py
+++ b/enterprise/signals/utils.py
@@ -4,7 +4,7 @@
 functions for use in other modules.
 """
 
-from __future__ import absolute_import, division, print_function, unicode_literals
+import logging
 
 import numpy as np
 import scipy.linalg as sl
@@ -16,22 +16,23 @@
 
 import enterprise
 from enterprise import constants as const
-from enterprise.signals.parameter import function
-from enterprise.signals.gp_priors import powerlaw, turnover  # noqa: F401
 from enterprise import signals as sigs  # noqa: F401
 from enterprise.signals.gp_bases import (  # noqa: F401
-    createfourierdesignmatrix_red,
     createfourierdesignmatrix_dm,
     createfourierdesignmatrix_env,
-    createfourierdesignmatrix_ephem,
     createfourierdesignmatrix_eph,
+    createfourierdesignmatrix_ephem,
+    createfourierdesignmatrix_red,
 )
+from enterprise.signals.gp_priors import powerlaw, turnover  # noqa: F401
+from enterprise.signals.parameter import function
 
+logger = logging.getLogger(__name__)
 
 try:
     from sksparse.cholmod import cholesky
-except:
-    print("You'll need sksparse for get_coefficients() with common signals!")
+except ImportError:
+    logger.warning("sksparse not installed. You'll need sksparse for get_coefficients() with common signals!")
 
 
 def get_coefficients(pta, params, n=1, phiinv_method="cliques", common_sparse=False):
diff --git a/enterprise/signals/white_signals.py b/enterprise/signals/white_signals.py
index d6703c1d..95b78871 100644
--- a/enterprise/signals/white_signals.py
+++ b/enterprise/signals/white_signals.py
@@ -3,7 +3,6 @@
 defined as the class of signals that only modifies the white noise matrix `N`.
 """
 
-from __future__ import absolute_import, division, print_function, unicode_literals
 
 import numpy as np
 import scipy.sparse
diff --git a/pyproject.toml b/pyproject.toml
index 571df8af..6dcc2e86 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,11 @@ exclude = '''
     | .enterprise
     | enterprise/src
   )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
 )
-'''
\ No newline at end of file
+'''
+[build-system]
+requires = [
+    "setuptools>=40.8.0",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 35be0917..0c6605b6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,8 @@
 numpy>=1.16.3
 scipy>=1.2.0
 ephem>=3.7.6.0
-Cython>=0.28.5
 jplephem==2.6
-setuptools>=40.0.0
 healpy>=1.14.0
-scikit-sparse>=0.4.2 --no-binary scikit-sparse
-git+https://github.com/nanograv/PINT.git@master#egg=pint-pulsar
-git+https://github.com/vallis/libstempo.git@master#egg=libstempo --install-option="--force-tempo2-install"
+scikit-sparse>=0.4.2
+pint-pulsar>=0.8.2
+git+https://github.com/vallis/libstempo.git@master#egg=libstempo
diff --git a/setup.py b/setup.py
index f1575ce0..54e380a0 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,14 @@
     history = history_file.read()
 
 requirements = [
-    # TODO: put package requirements here
+    "numpy>=1.16.3",
+    "scipy>=1.2.0",
+    "ephem>=3.7.6.0",
+    "jplephem==2.6",
+    "healpy>=1.14.0",
+    "scikit-sparse>=0.4.2",
+    "pint-pulsar>=0.8.2",
+    "libstempo @ git+https://github.com/vallis/libstempo.git@master#egg=libstempo",
 ]
 
 test_requirements = []
@@ -28,6 +35,7 @@
     package_dir={"enterprise": "enterprise"},
     include_package_data=True,
     package_data={"enterprise": ["datafiles/*", "datafiles/ephemeris/*", "datafiles/ng9/*", "datafiles/mdc_open1/*"]},
+    python_requires=">=3.6, <3.9",
     install_requires=requirements,
     license="MIT license",
     zip_safe=False,
diff --git a/tests/test_hierarchical_parameter.py b/tests/test_hierarchical_parameter.py
index b84f7bc7..9e767a0c 100644
--- a/tests/test_hierarchical_parameter.py
+++ b/tests/test_hierarchical_parameter.py
@@ -8,7 +8,6 @@
 Tests for hierarchical parameter functionality
 """
 
-from __future__ import division
 
 import unittest
 
diff --git a/tests/test_pulsar.py b/tests/test_pulsar.py
index 95cad51e..41fb6901 100644
--- a/tests/test_pulsar.py
+++ b/tests/test_pulsar.py
@@ -10,6 +10,8 @@
 """
 
 
+import os
+import shutil
 import unittest
 
 import numpy as np
@@ -31,6 +33,10 @@ def setUpClass(cls):
         # initialize Pulsar class
         cls.psr = Pulsar(datadir + "/B1855+09_NANOGrav_9yv1.gls.par", datadir + "/B1855+09_NANOGrav_9yv1.tim")
 
+    @classmethod
+    def tearDownClass(cls):
+        shutil.rmtree("pickle_dir")
+
     def test_residuals(self):
         """Check Residual shape."""
 
@@ -117,6 +123,8 @@ def test_to_pickle(self):
         with open("B1855+09.pkl", "rb") as f:
             pkl_psr = pickle.load(f)
 
+        os.remove("B1855+09.pkl")
+
         assert np.allclose(self.psr.residuals, pkl_psr.residuals, rtol=1e-10)
 
         self.psr.to_pickle("pickle_dir")
diff --git a/tests/test_vector_parameter.py b/tests/test_vector_parameter.py
index 77ae9faf..3d4b31d6 100644
--- a/tests/test_vector_parameter.py
+++ b/tests/test_vector_parameter.py
@@ -8,7 +8,6 @@
 Tests for vector parameter functionality
 """
 
-from __future__ import division
 
 import unittest
 

From d930cbf280424042c0b64ea459ee1f2b67f76ed7 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 14 Mar 2021 09:23:55 -0400
Subject: [PATCH 22/31] Naming to enterprise-pulsar for pypi

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 54e380a0..baf7b32a 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@
 
 
 setup(
-    name="enterprise",
+    name="enterprise-pulsar",
     version="3.0.0",
     description="ENTERPRISE (Enhanced Numerical Toolbox Enabling a Robust PulsaR Inference SuitE)",
     long_description=readme + "\n\n" + history,

From 104594fb36761bafc6e7a45321aeb28fd9ed15f6 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Fri, 19 Mar 2021 09:41:07 -0400
Subject: [PATCH 23/31] Small changes to makefile

---
 .github/workflows/ci_test.yml |  2 +-
 Makefile                      | 14 +++++---------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index 7fb1b01c..ca391db6 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -52,7 +52,7 @@ jobs:
     - name: Run lint
       run: make lint
     - name: Test with pytest
-      run: pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
+      run: make test
     - name: Codecov
       uses: codecov/codecov-action@v1
       with:
diff --git a/Makefile b/Makefile
index 43a59b17..3e7ba194 100644
--- a/Makefile
+++ b/Makefile
@@ -34,6 +34,8 @@ init:
 	@./.enterprise/bin/python3 -m pip install -r requirements_dev.txt -U
 	@./.enterprise/bin/python3 -m pre_commit install --install-hooks --overwrite
 	@./.enterprise/bin/python3 -m pip install -e .
+	@echo "run source .enterprise/bin/activate to activate environment"
+
 
 format:
 	black .
@@ -61,24 +63,18 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
+	rm -rf coverage.xml
 
 test: lint ## run tests quickly with the default Python
-	pytest -v --durations=10 --full-trace --cov-config .coveragerc --cov=enterprise tests
-
-#test-all: ## run tests on every Python version with tox
-#	tox
+	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml --cov-config .coveragerc --cov=enterprise tests
 
-coverage: ## check code coverage quickly with the default Python
-	coverage run --source enterprise setup.py test
 
-	coverage report -m
-	coverage html
+coverage: test ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html
 
 jupyter-docs:
 	jupyter nbconvert --template docs/nb-rst.tpl --to rst docs/_static/notebooks/*.ipynb --output-dir docs/
 	cp -r docs/_static/notebooks/img docs/
-	#jupyter nbconvert --template docs/nb-rst.tpl --to rst docs/_static/notebooks/tutorials/*.ipynb --output-dir docs/tutorials/
 
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/enterprise*.rst

From 9e807219e7d2b0d447f6a06ae5de927e1aa554f9 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 21 Mar 2021 07:58:04 -0400
Subject: [PATCH 24/31] Add coverage percent to test

---
 Makefile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 3e7ba194..1e69d5fe 100644
--- a/Makefile
+++ b/Makefile
@@ -65,8 +65,11 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 	rm -rf coverage.xml
 
+COV_COVERAGE_PERCENT ?= 85
 test: lint ## run tests quickly with the default Python
-	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml --cov-config .coveragerc --cov=enterprise tests
+	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml \
+		--cov-config .coveragerc --cov-fail-under=$(COV_COVERAGE_PERCENT) \
+		--cov=enterprise tests
 
 
 coverage: test ## check code coverage quickly with the default Python

From e0e767266b83e4c596481c9e05b7dae7c7627d67 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 21 Mar 2021 08:03:23 -0400
Subject: [PATCH 25/31] More cleaning of makefile

---
 Makefile | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index 1e69d5fe..93f3e3cf 100644
--- a/Makefile
+++ b/Makefile
@@ -71,11 +71,10 @@ test: lint ## run tests quickly with the default Python
 		--cov-config .coveragerc --cov-fail-under=$(COV_COVERAGE_PERCENT) \
 		--cov=enterprise tests
 
-
 coverage: test ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html
 
-jupyter-docs:
+jupyter-docs: ## biuld jupyter notebook docs
 	jupyter nbconvert --template docs/nb-rst.tpl --to rst docs/_static/notebooks/*.ipynb --output-dir docs/
 	cp -r docs/_static/notebooks/img docs/
 
@@ -91,14 +90,7 @@ docs: ## generate Sphinx HTML documentation, including API docs
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
-release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
-
 dist: clean ## builds source and wheel package
 	python setup.py sdist
 	python setup.py bdist_wheel
 	ls -l dist
-
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install

From 171d56c8fb37db52df0695a63315fc62b4a180a7 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 21 Mar 2021 09:01:24 -0400
Subject: [PATCH 26/31] log-level info in tests

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 93f3e3cf..e87c10eb 100644
--- a/Makefile
+++ b/Makefile
@@ -69,7 +69,7 @@ COV_COVERAGE_PERCENT ?= 85
 test: lint ## run tests quickly with the default Python
 	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml \
 		--cov-config .coveragerc --cov-fail-under=$(COV_COVERAGE_PERCENT) \
-		--cov=enterprise tests
+		--log-level=INFO --cov=enterprise tests
 
 coverage: test ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html

From 3b3c8c1310f52eb545cfcfa8b9c031c7a74ed6ea Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 21 Mar 2021 09:07:14 -0400
Subject: [PATCH 27/31] Udating contributing

---
 CONTRIBUTING.rst | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 27469e39..5fc127d7 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -72,14 +72,15 @@ Ready to contribute? Here's how to set up `enterprise` for local development.
    
     $ git pull upstream master
 
-4. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+4. This is how you set up your fork for local development::
+
+    .. note:: 
+        You will need to have ``tempo`` and ``suitesparse`` installed before  
+        running the commands below. 
 
-    $ mkvirtualenv enterprise
     $ cd enterprise/
-    $ pip install -r requirements_dev.txt
-    $ pip install -r requirements.txt
-    $ pip install libstempo --install-option="--with-tempo2=$TEMPO2"
-    $ python setup.py develop
+    $ make init
+    $ source .enterprise/bin/activate  
 
 5. Create a branch for local development::
 

From 4b61097b175d15a42b4eaebc36a0296281cbaa7d Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Sun, 21 Mar 2021 10:04:54 -0400
Subject: [PATCH 28/31] Fix contributing.rst

---
 CONTRIBUTING.rst | 4 +++-
 Makefile         | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 5fc127d7..ad6c38ec 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -72,12 +72,14 @@ Ready to contribute? Here's how to set up `enterprise` for local development.
    
     $ git pull upstream master
 
-4. This is how you set up your fork for local development::
+4. This is how you set up your fork for local development:
 
     .. note:: 
         You will need to have ``tempo`` and ``suitesparse`` installed before  
         running the commands below. 
 
+ ::
+
     $ cd enterprise/
     $ make init
     $ source .enterprise/bin/activate  
diff --git a/Makefile b/Makefile
index e87c10eb..93f3e3cf 100644
--- a/Makefile
+++ b/Makefile
@@ -69,7 +69,7 @@ COV_COVERAGE_PERCENT ?= 85
 test: lint ## run tests quickly with the default Python
 	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml \
 		--cov-config .coveragerc --cov-fail-under=$(COV_COVERAGE_PERCENT) \
-		--log-level=INFO --cov=enterprise tests
+		--cov=enterprise tests
 
 coverage: test ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html

From 2f0021a6ed1855a4da04f9e0c383de6afc40cd2c Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Wed, 24 Mar 2021 07:37:10 -0400
Subject: [PATCH 29/31] Adding libstempo pypi and dropping CI fail for coverage

---
 .github/workflows/ci_test.yml | 4 ++--
 requirements.txt              | 2 +-
 setup.py                      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
index ca391db6..b07cfcb3 100644
--- a/.github/workflows/ci_test.yml
+++ b/.github/workflows/ci_test.yml
@@ -55,8 +55,8 @@ jobs:
       run: make test
     - name: Codecov
       uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: true
+      #with:
+      #  fail_ci_if_error: true
 
 
   build:
diff --git a/requirements.txt b/requirements.txt
index 0c6605b6..692e4acd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,4 +5,4 @@ jplephem==2.6
 healpy>=1.14.0
 scikit-sparse>=0.4.2
 pint-pulsar>=0.8.2
-git+https://github.com/vallis/libstempo.git@master#egg=libstempo
+libstempo>=2.4.0
diff --git a/setup.py b/setup.py
index baf7b32a..5ab831a4 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
     "healpy>=1.14.0",
     "scikit-sparse>=0.4.2",
     "pint-pulsar>=0.8.2",
-    "libstempo @ git+https://github.com/vallis/libstempo.git@master#egg=libstempo",
+    "libstempo>=2.4.0",
 ]
 
 test_requirements = []

From f35c2a33b745e73cf7229315551343b37e9e61d9 Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Thu, 25 Mar 2021 08:04:32 -0400
Subject: [PATCH 30/31] adding no-cover to exceptions

---
 enterprise/pulsar.py              | 6 +++---
 enterprise/signals/signal_base.py | 2 +-
 enterprise/signals/utils.py       | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/enterprise/pulsar.py b/enterprise/pulsar.py
index 88bd7e9e..b35ac3bf 100644
--- a/enterprise/pulsar.py
+++ b/enterprise/pulsar.py
@@ -24,7 +24,7 @@
 try:
     import libstempo as t2
 except ImportError:
-    logger.warning("libstempo not installed. Will use PINT instead.")
+    logger.warning("libstempo not installed. Will use PINT instead.")  # pragma: no cover
     t2 = None
 
 try:
@@ -33,7 +33,7 @@
     from pint.residuals import Residuals as resids
     from pint.toa import TOAs
 except ImportError:
-    logger.warning("PINT not installed. Will use libstempo instead.")
+    logger.warning("PINT not installed. Will use libstempo instead.")  # pragma: no cover
     pint = None
 
 
@@ -574,4 +574,4 @@ def Pulsar(*args, **kwargs):
             os.chdir(cwd)
             return Tempo2Pulsar(t2pulsar, sort=sort, drop_t2pulsar=drop_t2pulsar, planets=planets)
     else:
-        logger.error("Unknown arguments {}".format(args))
+        logger.error("Unknown arguments {}".format(args))  # pragma: no cover
diff --git a/enterprise/signals/signal_base.py b/enterprise/signals/signal_base.py
index 3cc1cc2c..306db7e2 100644
--- a/enterprise/signals/signal_base.py
+++ b/enterprise/signals/signal_base.py
@@ -545,7 +545,7 @@ def _setpulsarcliques(self, slices, phis):
                         try:
                             self._cliques[slices[sc].start + phiind] = self._clcount
                             self._clcount = self._clcount + 1
-                        except Exception:
+                        except Exception:  # pragma: no cover
                             logger.exception("Exception raised in computing cliques")
                             logger.info(self._cliques.shape)
                             logger.info("phiind", phiind, len(phiind))
diff --git a/enterprise/signals/utils.py b/enterprise/signals/utils.py
index e90ea0cd..045ff9d4 100644
--- a/enterprise/signals/utils.py
+++ b/enterprise/signals/utils.py
@@ -31,7 +31,7 @@
 
 try:
     from sksparse.cholmod import cholesky
-except ImportError:
+except ImportError:  # pragma no cover
     logger.warning("sksparse not installed. You'll need sksparse for get_coefficients() with common signals!")
 
 

From d46f2e53ff90f18af23ed93010798aadc768a6ba Mon Sep 17 00:00:00 2001
From: Justin Ellis <justin.ellis18@gmail.com>
Date: Thu, 25 Mar 2021 08:14:17 -0400
Subject: [PATCH 31/31] Updated test

---
 enterprise/pulsar.py | 4 ++--
 tests/test_pulsar.py | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/enterprise/pulsar.py b/enterprise/pulsar.py
index b35ac3bf..11e0a40d 100644
--- a/enterprise/pulsar.py
+++ b/enterprise/pulsar.py
@@ -573,5 +573,5 @@ def Pulsar(*args, **kwargs):
             t2pulsar = t2.tempopulsar(relparfile, reltimfile, maxobs=maxobs, ephem=ephem, clk=clk)
             os.chdir(cwd)
             return Tempo2Pulsar(t2pulsar, sort=sort, drop_t2pulsar=drop_t2pulsar, planets=planets)
-    else:
-        logger.error("Unknown arguments {}".format(args))  # pragma: no cover
+
+    raise ValueError("Unknown arguments {}".format(args))
diff --git a/tests/test_pulsar.py b/tests/test_pulsar.py
index 41fb6901..d4a269f6 100644
--- a/tests/test_pulsar.py
+++ b/tests/test_pulsar.py
@@ -142,6 +142,12 @@ def test_wrong_input(self):
             msg = "Cannot find parfile wrong.par or timfile wrong.tim!"
             self.assertTrue(msg in context.exception)
 
+    def test_value_error(self):
+        """Test exception when unknown argument is given"""
+
+        with self.assertRaises(ValueError):
+            Pulsar(datadir + "/B1855+09_NANOGrav_9yv1.gls.par", datadir + "/B1855+09_NANOGrav_9yv1.time")
+
 
 class TestPulsarPint(TestPulsar):
     @classmethod