Full move to poetry, isort and added Codecov (#68)

* With poetry, no setup.py anymore

* GH action with poetry instead of requirements

* Fixed for poetry

* Using only poetry

* Trying to get poetry to work

* Try poetry via pip

* Split actions in jobs

* Using poetry action

* Using isort

* Using isort

* Fixed missing script for pip

* Updated

* Revert to install poetry via pip, not action

* Added Codecov

* Run coverage only once

* Testing if logic

* Fixed Python 3.6 for Codecov

* Fixed if

* Fixed if syntax

* Test syntax

* Test strategy.matrix

* Typos

* steps.matrix

* Back to last working state

* Removed requirements.txt

.github/workflows/check_acpype.yml

@@ -9,7 +9,7 @@ on:
       branches:
          - master
 jobs:
-   build:
+   check-test:
       runs-on: ubuntu-latest
       strategy:
          matrix:
@@ -23,6 +23,9 @@ jobs:
            with:
               python-version: ${{ matrix.python-version }}
 
+         # - name: Python Poetry Action
+         #   uses: abatilo/[email protected]
+
          - name: Cache pip
            uses: actions/cache@v2
            with:
@@ -49,26 +52,35 @@ jobs:
            run: |
               sudo apt-get install --no-install-recommends -y openbabel
 
-         - name: Install Pip
+         - name: Poetry install dependencies
            run: |
-              sudo apt-get install --no-install-recommends -y python3-pip
-              python3 -m pip install --upgrade pip
-              python3 -m pip install --upgrade openbabel-wheel
-              if [ -f requirements.txt ]; then python3 -m pip install -r requirements.txt; fi
-              # chmod +x acpype/acpype.py
-              # ln -s $PWD/run_acpype.py /usr/local/bin/acpype
+              pip3 install poetry
+              poetry add openbabel-wheel
+              poetry install
 
          - name: Lint with flake8
-           run: flake8 -v --count
+           run: poetry run flake8 -v --count
 
          - name: Check format with black
-           run: black --diff --check .
+           run: poetry run black --diff --check .
+
+         - name: Run isort
+           run: poetry run isort . --check-only --profile black
 
          - name: Test with PyTest
            run: |
-              # acpype -di test/AAA.pdb -c gas
-              pytest --color=yes
+              poetry run pytest --color=yes --cov=./ --cov-report=xml
+
+         - name: Upload coverage to Codecov
+           if: matrix.python-version == 3.6
+           uses: codecov/codecov-action@v2
+           with:
+              fail_ci_if_error: true
 
+   release:
+      needs: check-test
+      runs-on: ubuntu-latest
+      steps:
          - name: Get current date
            id: date
            run: echo "::set-output name=date::$(date +'%Y.%-m.%-d')"

.pre-commit-config.yaml

@@ -13,6 +13,12 @@ repos:
         language: system
         types: [python]
         require_serial: true
+      - id: isort
+        name: isort
+        entry: poetry run isort .
+        language: system
+        types: [python]
+        require_serial: true
       - id: ver_today
         name: ver_today
         entry: ./scripts/ver_today.sh

README.md

@@ -14,6 +14,8 @@
 [![GitHub Workflow Status](https://img.shields.io/github/workflow/status/alanwilter/acpype/check_acpype?style=plastic)](https://github.com/alanwilter/acpype)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=plastic)](https://github.com/pre-commit/pre-commit)
 [![Commits since release](https://img.shields.io/github/commits-since/alanwilter/acpype/2021.12.24/master?style=plastic)](https://github.com/alanwilter/acpype/commits/master)
+![Codecov](https://img.shields.io/codecov/c/github/alanwilter/acpype?style=plastic)
+![Codecov branch](https://img.shields.io/codecov/c/github/alanwilter/acpype/mv2poetry?style=plastic&token=a719f1fe-3a60-49a3-8804-9a44998c9e4a)
 <!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5601736.svg)](https://doi.org/10.1186/1756-0500-5-367)
 ![DOI](https://doi.org/10.1186/1756-0500-5-367) -->
 <!-- ![Scrutinizer code quality (GitHub/Bitbucket)](https://img.shields.io/scrutinizer/quality/g/alanwilter/acpype) -->

acpype/__init__.py

@@ -1,4 +1,4 @@
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
 # updated automatically via pre-commit git-hook
-__version__ = "2021.12.24"
+__version__ = "2021.12.25"

acpype/acs_api.py

@@ -1,13 +1,14 @@
-import sys
+import io
+import json
 import os
 import shutil
+import sys
 import time
-import io
 import traceback
-import json
-from acpype.topol import ACTopol, header
-from acpype.utils import while_replace, elapsedTime
+
 from acpype.params import MAXTIME
+from acpype.topol import ACTopol, header
+from acpype.utils import elapsedTime, while_replace
 
 em_mdp = io.StringIO()
 AC_frcmod = io.StringIO()

acpype/cli.py

@@ -51,16 +51,18 @@
     alanwilter _at_ gmail _dot_ com
 """
 
-import traceback
-import time
 import os
 import sys
+import time
+import traceback
 from shutil import rmtree
-from acpype.topol import MolTopol, ACTopol, header
-from acpype.parser_args import get_option_parser
-from acpype.utils import while_replace, elapsedTime, set_for_pip
+
+from acpype.logger import copy_log
+from acpype.logger import set_logging_conf as logger
 from acpype.params import binaries
-from acpype.logger import copy_log, set_logging_conf as logger
+from acpype.parser_args import get_option_parser
+from acpype.topol import ACTopol, MolTopol, header
+from acpype.utils import elapsedTime, set_for_pip, while_replace
 
 
 def chk_py_ver():

acpype/logger.py

@@ -1,7 +1,7 @@
+import logging
 import os
-from shutil import move
 import sys
-import logging
+from shutil import move
 from tempfile import NamedTemporaryFile
 
 tmpLogFile = NamedTemporaryFile().name

acpype/parser_args.py

@@ -1,5 +1,6 @@
 import argparse
-from acpype.params import usage, epilog, MAXTIME, outTopols
+
+from acpype.params import MAXTIME, epilog, outTopols, usage
 
 
 def get_option_parser():

acpype/topol.py

@@ -1,21 +1,49 @@
-import re
-import signal
+import abc
+import array
 import math
 import os
 import pickle
+import re
+import signal
 import subprocess as sub
-import abc
-import array
 from datetime import datetime
 from shutil import copy2, rmtree, which
-from acpype.mol import Atom, Angle, AtomType, Bond, Dihedral
+
 from acpype import __version__ as version
-from acpype.params import minDist, minDist2, maxDist, maxDist2, MAXTIME, TLEAP_TEMPLATE, leapAmberFile, radPi, cal
-from acpype.params import binaries, ionOrSolResNameList, outTopols, qDict, qConv, diffTol, specialGaffAtoms
-from acpype.params import dictAtomTypeAmb2OplsGmxCode, dictAtomTypeGaff2OplsGmxCode, oplsCode2AtomTypeDict
-from acpype.utils import _getoutput, while_replace, distanceAA, job_pids_family, checkOpenBabelVersion
-from acpype.utils import find_bin, elapsedTime, imprDihAngle, parmMerge
 from acpype.logger import set_logging_conf as logger
+from acpype.mol import Angle, Atom, AtomType, Bond, Dihedral
+from acpype.params import (
+    MAXTIME,
+    TLEAP_TEMPLATE,
+    binaries,
+    cal,
+    dictAtomTypeAmb2OplsGmxCode,
+    dictAtomTypeGaff2OplsGmxCode,
+    diffTol,
+    ionOrSolResNameList,
+    leapAmberFile,
+    maxDist,
+    maxDist2,
+    minDist,
+    minDist2,
+    oplsCode2AtomTypeDict,
+    outTopols,
+    qConv,
+    qDict,
+    radPi,
+    specialGaffAtoms,
+)
+from acpype.utils import (
+    _getoutput,
+    checkOpenBabelVersion,
+    distanceAA,
+    elapsedTime,
+    find_bin,
+    imprDihAngle,
+    job_pids_family,
+    parmMerge,
+    while_replace,
+)
 
 year = datetime.today().year
 tag = version

acpype/utils.py

@@ -1,8 +1,9 @@
-import os
-import sys
 import math
+import os
 import subprocess as sub
+import sys
 from shutil import which
+
 from acpype.params import Pi
 
 
@@ -12,9 +13,10 @@ def find_bin(abin):
 
 def checkOpenBabelVersion():
     "check openbabel version"
-    import openbabel as obl
     import warnings
 
+    import openbabel as obl
+
     warnings.filterwarnings("ignore")
     return int(obl.OBReleaseVersion().replace(".", ""))
 
@@ -248,7 +250,10 @@ def job_pids_family(jpid):
 
 
 def _getoutput(cmd):
-    """to simulate commands.getoutput in order to work with python 2.6 up to 3.x"""
+    """
+    To simulate commands.getoutput
+    shell=True is necessary despite security issues
+    """
     out = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE).communicate()[0][:-1]
     return out.decode()
 

legacy/CcpnToAcpype.py

@@ -1,17 +1,18 @@
 from __future__ import print_function
-from builtins import range
-from builtins import object
-from shutil import rmtree
-from acpype.cli import elapsedTime, header, ACTopol
-import time
-import traceback
-import sys
+
 import os
-import string
 import random
+import string
+import sys
+import time
+import traceback
+from builtins import object, range
+from shutil import rmtree
 
-from ccpnmr.format.converters import PdbFormat  # type: ignore
 from ccpnmr.format.converters import Mol2Format  # type: ignore
+from ccpnmr.format.converters import PdbFormat  # type: ignore
+
+from acpype.cli import ACTopol, elapsedTime, header
 
 letters = string.ascii_letters