Update

.github/workflows/CI.yaml

@@ -18,84 +18,87 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
 
-jobs:
-  linux:
-    runs-on: ubuntu-latest
-    steps:
-      - run: sudo apt-get install gfortran
-      - run: gfortran --version
-
-  windows:
-    runs-on: windows-latest
-    steps:
-      - run: choco install mingw
-
+jobs: 
   test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
+      - uses: actions/checkout@v4
 
-# Not relevant now, but may be needed when f2py issues are solved, for now only numba
-#    - name: Set up msys for Windows
-#      if: matrix.os == 'windows-latest'
-#      uses: msys2/setup-msys2@v2
-#      with:
-#        update: true
-#        install: >-
-#          mingw-w64-x86_64-gcc-fortran
-#          mingw-w64-x86_64-gcc
-
-    - uses: actions/checkout@v2
-
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
 
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
+      # More info on options: https://github.com/conda-incubator/setup-miniconda
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: devtools/conda-envs/test_env.yaml
+          activate-environment: test
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=${{ matrix.python-version }}
 
-    - name: Testing Dependencies
-      shell: bash -l {0}
-      run: |
-        python -m pip install -U pytest pytest-cov codecov
-
-    - name: Install gfortran on mac
-      if: matrix.os == 'macOS-latest'
-      shell: bash -l {0}
-      run: |
-        conda install -c conda-forge gfortran_osx-64
+      - name: Testing Dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install -U pytest pytest-cov codecov
 
-    - name: Install package
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install -e . --no-deps -vvv
-        conda list
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e . --no-deps -vvv
+          conda list
 
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        ls -a despasito/equations_of_state/saft/compiled_modules
-        pytest -vvv --cov=despasito --cov-report=xml --color=yes despasito/tests/
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          ls -a despasito/equations_of_state/saft/compiled_modules
+          pytest -vvv --cov=despasito --cov-report=xml --color=yes despasito/tests/
+
+      - name: CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+
+      - name: Flake8
+        shell: bash -l {0}
+        run: |
+          python -m flake8 despasito --count --ignore=E741,W503 --max-line-length=92 --show-source --statistics
 
-    - name: CodeCov
-      uses: codecov/codecov-action@v1
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.gitignore

@@ -7,6 +7,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.DS_Store
 
 # C extensions
 *.so

.readthedocs.yml

@@ -4,22 +4,19 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: docs/requirements
-
-#conda:
-#    environment: devtools/conda-envs/readthedocs_env.yaml

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "python.testing.pytestArgs": [],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

README.md

@@ -6,7 +6,6 @@ DESPASITO
 [![GitHub Actions Build Status](https://github.com/jaclark5/despasito/workflows/CI/badge.svg)](https://github.com/jaclark5/despasito/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/jaclark5/DESPASITO/branch/master/graph/badge.svg)](https://codecov.io/gh/jaclark5/DESPASITO/branch/master)
 [![Documentation Status](https://readthedocs.org/projects/despasito/badge/?version=latest)](https://despasito.readthedocs.io/en/latest/?badge=latest)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/jaclark5/despasito.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/jaclark5/despasito/context:python)
 
 DESPASITO: Determining Equilibrium State and Parametrization Application for SAFT, Intended for Thermodynamic Output
 
@@ -44,7 +43,7 @@ Options
 
  * Step 1: Install the prerequisites listed above.
  * Step 2: Download the master branch from our github page as a zip file, or clone it with git via ``git clone https://github.com/jaclark5/despasito`` to your working directory.
- * Step 3: Install with ``pip install despasito/.``, or change directories and run ``pip install .``.
+ * Step 3: Install with ``pip install despasito/.``, or change directories and run ``pip install -e .``.
 
 **NOTE** If [pip](https://pip.pypa.io/en/stable/) is unavailable, follow the instructions outlined [here](https://pip.pypa.io/en/stable/installing/) for installation.
 

despasito/__init__.py

@@ -1,10 +1,12 @@
 """
 DESPASITO
-DESPASITO: Determining Equilibrium State and Parametrization Application for SAFT, Intended for Thermodynamic Output
+DESPASITO: Determining Equilibrium State and Parametrization Application for SAFT,
+Intended for Thermodynamic Output
 """
 
-# Add imports here
-from .main import run
+import os
+import logging
+import logging.handlers
 
 # Handle versioneer
 from ._version import get_versions
@@ -14,10 +16,6 @@
 __git_revision__ = versions["full-revisionid"]
 del get_versions, versions
 
-import logging
-import logging.handlers
-import os
-
 logger = logging.getLogger()
 logger.setLevel(30)
 
@@ -26,16 +24,26 @@ def initiate_logger(console=None, log_file=None, verbose=30):
     """
     Initiate a logging handler if more detail on the calculations is desired.
 
-    This function is useful when DESPASITO is used as an imported package. If a handler of the given type is already present, nothing is done, as is the case when the input file schema is used. If either handler is given a value of False, the handler of that type is removed. 
+    This function is useful when DESPASITO is used as an imported package. If a handler
+    of the given type is already present, nothing is done, as is the case when the
+    input file schema is used. If either handler is given a value of False, the handler
+    of that type is removed.
 
     Parameters
     ----------
     console : bool, Optional, default=None
-        Initiates a stream handler to print to a console. If True, this handler is initiated. If it is False, then any StreamHandler is removed.
+        Initiates a stream handler to print to a console. If True, this handler is
+        initiated. If it is False, then any StreamHandler is removed.
     log_file : bool/str, Optional, default=None
-        If log output should be recorded in a file, set this keyword to either True or to a name for the log file. If True, the file name 'despasito.log' is used. Note that if a file with the same name already exists, it will be deleted.
+        If log output should be recorded in a file, set this keyword to either True or
+        to a name for the log file. If True, the file name 'despasito.log' is used.
+        Note that if a file with the same name already exists, it will be deleted.
     verbose : int, Optional, default=30
-        The verbosity of logging information can be set to any supported representation of the `logging level <https://docs.python.org/3/library/logging.html#logging-levels>`_.  
+        The verbosity of logging information can be set to any supported representation
+        of the
+        `logging level <LOGGER>`_.
+
+    .. _LOGGER: https://docs.python.org/3/library/logging.html#logging-levels
     """
 
     logger.setLevel(verbose)
@@ -50,7 +58,7 @@ def initiate_logger(console=None, log_file=None, verbose=30):
             handler_console = tmp
 
     # Set up logging to console
-    if console and handler_console == None:
+    if console and handler_console is None:
         console_handler = logging.StreamHandler()  # sys.stderr
         console_handler.setFormatter(
             logging.Formatter("[%(levelname)s](%(name)s): %(message)s")
@@ -59,14 +67,14 @@ def initiate_logger(console=None, log_file=None, verbose=30):
         logger.addHandler(console_handler)
     elif console:
         logger.warning("StreamHandler already exists")
-    elif handler_console == False:
+    elif handler_console is not None:
         handler_console.close()
         logger.removeHandler(handler_console)
 
     # Rotating File Handler
-    if log_file is not None and handler_logfile == None:
+    if log_file is not None and handler_logfile is None:
 
-        if type(log_file) != str:
+        if not isinstance(log_file, str):
             log_file = "despasito.log"
 
         if os.path.isfile(log_file):
@@ -75,13 +83,14 @@ def initiate_logger(console=None, log_file=None, verbose=30):
         log_file_handler = logging.handlers.RotatingFileHandler(log_file)
         log_file_handler.setFormatter(
             logging.Formatter(
-                "%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): %(message)s"
+                "%(asctime)s [%(levelname)s](%(name)s:%(funcName)s:%(lineno)d): "
+                + "%(message)s"
             )
         )
         log_file_handler.setLevel(verbose)
         logger.addHandler(log_file_handler)
     elif log_file:
         logger.warning("RotatingFileHandler already exists")
-    elif handler_logfile == False:
+    elif not handler_logfile:
         handler_logfile.close()
         logger.removeHandler(handler_logfile)

despasito/__main__.py

@@ -10,7 +10,7 @@
 parser = get_parser()
 args = parser.parse_args()
 
-## Extract arguments
+# Extract arguments
 if args.verbose == 0:
     args.verbose = 20
 elif args.verbose < 4:
@@ -56,7 +56,7 @@
 kwargs["numba"] = args.numba
 logging.info("Use Cython: {}".format(args.cython))
 kwargs["cython"] = args.cython
-logging.info("Pure Python (no Fortran): {}".format(args.python))
+logging.info("Pure Python: {}".format(args.python))
 kwargs["python"] = args.python
 
 kwargs["MultiprocessingObject"] = MultiprocessingJob(ncores=args.ncores)

despasito/_version.py

@@ -120,7 +120,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
             return {
-                "version": dirname[len(parentdir_prefix) :],
+                "version": dirname[len(parentdir_prefix):],
                 "full-revisionid": None,
                 "dirty": False,
                 "error": None,
@@ -190,7 +190,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -207,7 +207,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
             if verbose:
                 print("picking %s" % r)
             return {
@@ -307,7 +307,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
                 tag_prefix,
             )
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))