Merge pull request #35 from xtrojak/conda-env

Conda env

.github/workflows/python-package-conda.yml

@@ -0,0 +1,37 @@
+name: Python Package using Conda
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file conda/environment-dev.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest pytest-cov
+        pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml

conda/environment-build.yml

@@ -0,0 +1,15 @@
+name: pyMSPannotator
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python >=3.7,<3.9
+  - matchms >=0.9.1
+  - pandas
+  - scipy
+  - requests
+  - aiohttp
+  - asyncstdlib
+  - frozendict
+  - tabulate

conda/environment-dev.yml

@@ -0,0 +1,19 @@
+name: pyMSPannotator
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python >=3.7,<3.9
+  - matchms >=0.9.1
+  - pandas
+  - scipy
+  - requests
+  - aiohttp
+  - asyncstdlib
+  - frozendict
+  - tabulate
+  - mock
+  - pytest
+  - pytest-aiohttp
+  - pytest-cov

conda/meta.yml

@@ -0,0 +1,62 @@
+{% set name = "pyMSPannotator" %}
+{% set version = "0.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  path: ..
+
+extra:
+  channels:
+    - conda-forge
+    - bioconda
+
+build:
+  noarch: python
+  preserve_egg_dir: True
+  number: 0
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv
+
+requirements:
+  build:
+    - conda-build
+    - conda-verify
+    - pytest-runner
+    - python
+    - setuptools
+  host:
+    - python >=3.7,<3.9
+    - pip
+    - pytest-runner
+    - setuptools
+  run:
+    - python >=3.7,<3.9
+    - matchms >=0.9.1
+    - pandas
+    - scipy
+    - requests
+    - aiohttp
+    - asyncstdlib
+    - frozendict
+    - tabulate
+    - mock
+    - pytest
+    - pytest-aiohttp
+    - pytest-cov
+
+test:
+  imports:
+    - pyMSPannotator
+
+about:
+  home: https://github.com/RECETOX/pyMSPannotator
+  license: MIT
+  license_file: LICENSE
+  summary: Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files (Python version).
+  dev_url: https://github.com/RECETOX/pyMSPannotator
+
+extra:
+  recipe-maintainers:
+    - xtrojak

app.py → pyMSPannotator/app.py

@@ -1,13 +1,13 @@
 import asyncio
 import aiohttp
 
-from libs.Annotator import Annotator
-from libs.Curator import Curator
-from libs.Spectra import Spectra
-from libs.utils import logger
-from libs.utils.Errors import UnknownService, UnknownSpectraFormat
-from libs.utils.Job import convert_to_jobs
-from libs.services import *
+from pyMSPannotator.libs.Annotator import Annotator
+from pyMSPannotator.libs.Curator import Curator
+from pyMSPannotator.libs.Spectra import Spectra
+from pyMSPannotator.libs.utils import logger
+from pyMSPannotator.libs.utils.Errors import UnknownService, UnknownSpectraFormat
+from pyMSPannotator.libs.utils.Job import convert_to_jobs
+from pyMSPannotator.libs.services import *
 
 
 class Application:

libs/Annotator.py → pyMSPannotator/libs/Annotator.py

@@ -1,7 +1,7 @@
-from libs.utils import logger
-from libs.utils.Errors import ConversionNotSupported, TargetAttributeNotRetrieved, SourceAttributeNotAvailable, \
-    ServiceNotAvailable, UnknownResponse
-from libs.utils.Logger import LogWarning
+from pyMSPannotator.libs.utils import logger
+from pyMSPannotator.libs.utils.Errors import ConversionNotSupported, TargetAttributeNotRetrieved, \
+    SourceAttributeNotAvailable, ServiceNotAvailable, UnknownResponse
+from pyMSPannotator.libs.utils.Logger import LogWarning
 
 
 class Annotator:

libs/services/CIR.py → pyMSPannotator/libs/services/CIR.py

@@ -1,4 +1,4 @@
-from libs.services.Converter import Converter
+from pyMSPannotator.libs.services.Converter import Converter
 
 
 class CIR(Converter):

libs/services/CTS.py → pyMSPannotator/libs/services/CTS.py

@@ -1,6 +1,6 @@
 import json
 
-from libs.services.Converter import Converter
+from pyMSPannotator.libs.services.Converter import Converter
 
 
 class CTS(Converter):
@@ -17,7 +17,7 @@ def __init__(self, session):
                        ('inchikey', 'iupac_name', 'from_inchikey')]
         self.create_top_level_conversion_methods(conversions)
 
-    ### top level methods defining allowed conversions
+    # top level methods defining allowed conversions
 
     async def casno_to_inchikey(self, cas_number):
         """
@@ -44,8 +44,6 @@ async def name_to_inchikey(self, name):
         if response:
             return self.parse_inchikey(response)
 
-    ###
-
     async def from_inchikey(self, inchikey):
         """
         Convert InChiKey to all possible attributes using CTS compound service

libs/services/Converter.py → pyMSPannotator/libs/services/Converter.py

@@ -4,8 +4,8 @@
 
 from aiohttp.client_exceptions import ServerDisconnectedError
 
-from libs.utils import logger
-from libs.utils.Errors import TargetAttributeNotRetrieved, ServiceNotAvailable, UnknownResponse
+from pyMSPannotator.libs.utils import logger
+from pyMSPannotator.libs.utils.Errors import TargetAttributeNotRetrieved, ServiceNotAvailable, UnknownResponse
 
 
 class Converter:

libs/services/NLM.py → pyMSPannotator/libs/services/NLM.py

@@ -2,7 +2,7 @@
 
 import pandas as pd
 
-from libs.services.Converter import Converter
+from pyMSPannotator.libs.services.Converter import Converter
 
 
 class NLM(Converter):

libs/services/PubChem.py → pyMSPannotator/libs/services/PubChem.py

@@ -1,6 +1,6 @@
 import asyncio
 
-from libs.services.Converter import Converter
+from pyMSPannotator.libs.services.Converter import Converter
 from frozendict import frozendict
 
 

pyMSPannotator/libs/services/__init__.py

@@ -0,0 +1,4 @@
+from pyMSPannotator.libs.services.CIR import CIR
+from pyMSPannotator.libs.services.CTS import CTS
+from pyMSPannotator.libs.services.NLM import NLM
+from pyMSPannotator.libs.services.PubChem import PubChem

libs/utils/Job.py → pyMSPannotator/libs/utils/Job.py

@@ -1,4 +1,4 @@
-from libs.utils.Errors import ConversionNotSupported, SourceAttributeNotAvailable
+from pyMSPannotator.libs.utils.Errors import ConversionNotSupported, SourceAttributeNotAvailable
 
 
 class Job:

libs/utils/Logger.py → pyMSPannotator/libs/utils/Logger.py

@@ -2,7 +2,7 @@
 import logging
 from asyncio import Queue
 
-from libs.utils.Metrics import Metrics
+from pyMSPannotator.libs.utils.Metrics import Metrics
 
 
 class Logger:

pyMSPannotator/libs/utils/__init__.py

@@ -0,0 +1,3 @@
+from pyMSPannotator.libs.utils.Logger import Logger
+
+logger = Logger()

setup.py

@@ -0,0 +1,24 @@
+from setuptools import setup, find_packages
+
+setup(name='pyMSPannotator',
+      version='0.1',
+      description='Repository for tool that adds more annotations '
+                  '(e.g. SMILES, InChI, CAS number) to MSP files (Python version).',
+      url='https://github.com/RECETOX/pyMSPannotator',
+      author='Matej Trojak',
+      author_email='matej.trojak@recetox.muni.cz',
+      license='MIT',
+      packages=find_packages(exclude=['*tests*']),
+      zip_safe=False,
+      test_suite="tests",
+      python_requires='>=3.7',
+      install_requires=[
+            "matchms",
+            "requests",
+            "pandas",
+            "aiohttp",
+            "asyncstdlib",
+            "frozendict",
+            "tabulate"
+      ]
+      )

tests/test_CIR.py

@@ -1,8 +1,8 @@
 import asyncio
 import pytest
 
-from libs.services.CIR import CIR
-from libs.utils.Errors import UnknownResponse
+from pyMSPannotator.libs.services.CIR import CIR
+from pyMSPannotator.libs.utils.Errors import UnknownResponse
 from tests.utils import wrap_with_session
 
 

tests/test_CTS.py

@@ -2,17 +2,17 @@
 import json
 import pytest
 
-from libs.services.CTS import CTS
-from libs.utils.Errors import UnknownResponse
+from pyMSPannotator.libs.services.CTS import CTS
+from pyMSPannotator.libs.utils.Errors import UnknownResponse
 from tests.utils import wrap_with_session
 
 
 @pytest.mark.parametrize('arg, value, expected, method', [
     ['inchikey', '7783-89-3', 'XQLMNMQWVCXIKR-UHFFFAOYSA-M', 'casno_to_inchikey'],
     ['inchi', 'XQLMNMQWVCXIKR-UHFFFAOYSA-M', 'InChI=1S/Ag.BrHO3/c;2-1(3)4/h;(H,2,3,4)/q+1;/p-1', 'inchikey_to_inchi'],
     ['inchikey', 'L-Alanine', 'QNAYBMKLOCPYGJ-REOHCLBHSA-N', 'name_to_inchikey'],
-    ['name', 'QNAYBMKLOCPYGJ-REOHCLBHSA-N', 'L-2-Aminopropanoic acid', 'inchikey_to_name'],
-    ['iupac_name', 'QNAYBMKLOCPYGJ-REOHCLBHSA-N', '(2S)-2-aminopropanoic acid', 'inchikey_to_iupac_name']
+    ['name', 'QNAYBMKLOCPYGJ-REOHCLBHSA-N', 'L-ALANINE', 'inchikey_to_name'],
+    ['iupac_name', 'QNAYBMKLOCPYGJ-REOHCLBHSA-N', '(2S)-2-azaniumylpropanoate', 'inchikey_to_iupac_name']
 ])
 def test_correct_behavior(arg, value, expected, method):
     assert asyncio.run(wrap_with_session(CTS, method, [value]))[arg] == expected

tests/test_MSP.py

@@ -1,7 +1,7 @@
 import asyncio
 from copy import copy
 
-from app import Application
+from pyMSPannotator.app import Application
 
 
 def test_annotate_MSP_file():

tests/test_NLM.py

@@ -3,8 +3,8 @@
 import pandas as pd
 import pytest
 
-from libs.services.NLM import NLM
-from libs.utils.Errors import UnknownResponse
+from pyMSPannotator.libs.services.NLM import NLM
+from pyMSPannotator.libs.utils.Errors import UnknownResponse
 from tests.utils import wrap_with_session
 
 

tests/test_annotator.py

@@ -2,9 +2,9 @@
 import pytest
 import mock
 
-from libs.Annotator import Annotator
-from libs.utils.Errors import TargetAttributeNotRetrieved
-from libs.utils.Job import Job
+from pyMSPannotator.libs.Annotator import Annotator
+from pyMSPannotator.libs.utils.Errors import TargetAttributeNotRetrieved
+from pyMSPannotator.libs.utils.Job import Job
 
 
 @pytest.mark.parametrize('data, expected, repeat, mocked', [

tests/test_converter.py

@@ -6,9 +6,9 @@
 from aiohttp import ServerDisconnectedError
 from aiohttp import web
 
-from libs.services import CTS, CIR
-from libs.services.Converter import Converter
-from libs.utils.Errors import TargetAttributeNotRetrieved, UnknownResponse
+from pyMSPannotator.libs.services import CTS, CIR
+from pyMSPannotator.libs.services.Converter import Converter
+from pyMSPannotator.libs.utils.Errors import TargetAttributeNotRetrieved, UnknownResponse
 
 
 def test_query_the_service():

tests/test_curator.py

@@ -1,4 +1,4 @@
-from libs.Curator import Curator
+from pyMSPannotator.libs.Curator import Curator
 
 
 def test_fix_cas_number():

tests/test_pubchem.py

@@ -1,7 +1,7 @@
 import asyncio
 import pytest
 
-from libs.services.PubChem import PubChem
+from pyMSPannotator.libs.services.PubChem import PubChem
 from frozendict import frozendict
 
 from tests.utils import wrap_with_session