Refactor code.

.github/workflows/ci.yml

@@ -0,0 +1,50 @@
+name: Python CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      matrix:
+        python-version: [3.7]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get install -qq phyml
+        pip install --upgrade pip setuptools wheel
+        pip install --only-binary=numpy,scipy numpy scipy
+        pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
+        pip install -r requirements.txt
+        pip install .
+
+    - name: Run tests
+      run: pytest --cov-report=xml --cov=OrthoEvol tests/
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        fail_ci_if_error: true
+
+    - name: Notify failure
+      if: failure()
+      run: echo "Build failed"

.travis.yml

@@ -5,32 +5,30 @@ notifications:
   email: [email protected]
 jobs:
   include:
-    - python: 3.5
-      dist: trusty
-      install:
-        - pip install --upgrade pip setuptools wheel
-        - pip install --only-binary=numpy,scipy numpy scipy
-        - pip install matplotlib ipython jupyter sympy pytest codecov "pytest-cov<=2.6.0"
-        - pip install -r requirements.txt
-        - pip install .
-    - python: 3.6
+    - python: 3.7
       dist: xenial
+      before_install:
+        - sudo apt-get install -qq phyml
       install:
         - pip install --upgrade pip setuptools wheel
         - pip install --only-binary=numpy,scipy numpy scipy
         - pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
         - pip install -r requirements.txt
         - pip install .
-    - python: 3.7
+    - python: 3.8
       dist: xenial
+      before_install:
+        - sudo apt-get install -qq phyml
       install:
         - pip install --upgrade pip setuptools wheel
         - pip install --only-binary=numpy,scipy numpy scipy
         - pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
         - pip install -r requirements.txt
         - pip install .
-    - python: 3.8
+    - python: 3.9
       dist: xenial
+      before_install:
+        - sudo apt-get install -qq phyml
       install:
         - pip install --upgrade pip setuptools wheel
         - pip install --only-binary=numpy,scipy numpy scipy

OrthoEvol/Cookies/new_website/tasks.py

@@ -1,77 +1,73 @@
-#!/usr/bin/env python
-"""Invoke tasks."""
-import os
-import json
-import shutil
-import webbrowser
-
-from invoke import task
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(HERE, 'cookiecutter.json'), 'r') as fp:
-    COOKIECUTTER_SETTINGS = json.load(fp)
-# Match default value of website_name from cookiecutter.json
-COOKIE = os.path.join(HERE, COOKIECUTTER_SETTINGS['website_name'])
-AUTOAPP = os.path.join(COOKIE, 'autoapp.py')
-REQUIREMENTS = os.path.join(COOKIE, 'requirements', 'dev.txt')
-
-
-@task
-def build(ctx):
-    """Build the cookiecutter.
-
-    :param ctx: 
-
-    """
-    ctx.run('cookiecutter {0} --no-input'.format(HERE))
-
-
-@task
-def clean(ctx):
-    """Clean out generated cookiecutter.
-
-    :param ctx: 
-
-    """
-    if os.path.exists(COOKIE):
-        shutil.rmtree(COOKIE)
-        print('Removed {0}'.format(COOKIE))
-    else:
-        print('App directory does not exist. Skipping.')
-
-
-def _run_flask_command(ctx, command):
-    """
-
-    :param ctx: 
-    :param command: 
-
-    """
-    ctx.run('FLASK_APP={0} flask {1}'.format(AUTOAPP, command), echo=True)
-
-
-@task(pre=[clean, build])
-def test(ctx):
-    """Run lint commands and tests.
-
-    :param ctx: 
-
-    """
-    ctx.run('pip install -r {0} --ignore-installed'.format(REQUIREMENTS),
-            echo=True)
-    os.chdir(COOKIE)
-    _run_flask_command(ctx, 'lint')
-    _run_flask_command(ctx, 'test')
-
-@task
-def readme(ctx, browse=False):
-    """
-
-    :param ctx: 
-    :param browse:  (Default value = False)
-
-    """
-    ctx.run("rst2html.py README.rst > README.html")
-    if browse:
-        webbrowser.open_new_tab('README.html')
-
+#!/usr/bin/env python
+"""Invoke tasks."""
+
+import os
+import json
+import shutil
+import webbrowser
+
+from invoke import task
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+# Load the settings from cookiecutter.json
+with open(os.path.join(HERE, 'cookiecutter.json'), 'r') as fp:
+    COOKIECUTTER_SETTINGS = json.load(fp)
+
+# Match default value of website_name from cookiecutter.json
+COOKIE = os.path.join(HERE, COOKIECUTTER_SETTINGS['website_name'])
+
+# Path to autoapp.py file
+AUTOAPP = os.path.join(COOKIE, 'autoapp.py')
+
+# Path to dev requirements file
+REQUIREMENTS = os.path.join(COOKIE, 'requirements', 'dev.txt')
+
+@task
+def build(ctx):
+    """Build the cookiecutter."""
+
+    # Run cookiecutter with no input
+    ctx.run(f'cookiecutter {HERE} --no-input')
+
+@task
+def clean(ctx):
+    """Clean out generated cookiecutter."""
+
+    # Remove the cookiecutter directory if it exists
+    if os.path.exists(COOKIE):
+        shutil.rmtree(COOKIE)
+        print(f'Removed {COOKIE}')
+    else:
+        print('App directory does not exist. Skipping.')
+
+def _run_flask_command(ctx, command):
+    """Run a Flask command."""
+
+    # Run the specified Flask command
+    ctx.run(f'FLASK_APP={AUTOAPP} flask {command}', echo=True)
+
+@task(pre=[clean, build])
+def test(ctx):
+    """Run lint commands and tests."""
+
+    # Install dev requirements
+    ctx.run(f'pip install -r {REQUIREMENTS} --ignore-installed', echo=True)
+
+    # Change to the cookiecutter directory
+    os.chdir(COOKIE)
+
+    # Run lint and test commands
+    _run_flask_command(ctx, 'lint')
+    _run_flask_command(ctx, 'test')
+
+@task
+def readme(ctx, browse=False):
+    """Convert the README to HTML."""
+
+    # Convert the README to HTML
+    ctx.run("rst2html.py README.rst > README.html")
+
+    # Open the HTML file in a web browser if specified
+    if browse:
+        webbrowser.open_new_tab('README.html')

OrthoEvol/Manager/db_mana_test.py

@@ -7,43 +7,49 @@
 import getpass
 from datetime import datetime as d
 import os
-_jobname = "jobname"
 
-# Set up project management
-pm_config_file = resource_filename(yml.__name__, "initialize_new.yml")
-with open(pm_config_file, 'r') as f:
-    pm_config = yaml.load(f, Loader=yaml.FullLoader)
-pm = ProjectManagement(**pm_config["Management_config"])
+# Define job name
+job_name = "jobname"
 
-# Set up database management
-db_config_file = resource_filename(yml.__name__, "databases.yml")
-with open(db_config_file, 'r') as f:
-    db_config = yaml.load(f, Loader=yaml.FullLoader)
+# Function to load configuration from YAML file
+def load_config(file_name):
+    file_path = resource_filename(yml.__name__, file_name)
+    with open(file_path, 'r') as file:
+        return yaml.load(file, Loader=yaml.FullLoader)
+
+# Load project management configuration
+pm_config = load_config("initialize_new.yml")
+project_manager = ProjectManagement(**pm_config["Management_config"])
+
+# Load and update database management configuration
+db_config = load_config("databases.yml")
 db_config.update(pm_config)
-db_config['Database_config']['Full']['NCBI']['NCBI_refseq_release']['upload_number'] = 12
-db_config['Database_config']['Full']['NCBI']['NCBI_refseq_release']['pbs_dict'] = {
-            'author': getpass.getuser(),
-            'description': 'This is a default pbs job.',
-            'date': d.now().strftime('%a %b %d %I:%M:%S %p %Y'),
-            'proj_name': 'OrthoEvol',
-            'select': '1',
-            'memgb': '6gb',
-            'cput': '72:00:00',
-            'wt': '2000:00:00',
-            'job_name': _jobname,
-            'outfile': _jobname + '.o',
-            'errfile': _jobname + '.e',
-            'script': _jobname,
-            'log_name': _jobname,
-            'pbsworkdir': os.getcwd(),
-            'cmd': 'python3.6 ' + os.path.join(os.getcwd(), _jobname + '.py'),
-            'email': 'n/a'
-             }
-# Generate main config file for this job
-config_file = pm.user_log / Path("upload_config.yml")
-with open(str(config_file), 'w') as cf:
-    yaml.dump(db_config, cf, default_flow_style=False)
+ncbi_config = db_config['Database_config']['Full']['NCBI']['NCBI_refseq_release']
+ncbi_config['upload_number'] = 12
+ncbi_config['pbs_dict'] = {
+    'author': getpass.getuser(),
+    'description': 'This is a default pbs job.',
+    'date': d.now().strftime('%a %b %d %I:%M:%S %p %Y'),
+    'proj_name': 'OrthoEvol',
+    'select': '1',
+    'memgb': '6gb',
+    'cput': '72:00:00',
+    'wt': '2000:00:00',
+    'job_name': job_name,
+    'outfile': job_name + '.o',
+    'errfile': job_name + '.e',
+    'script': job_name,
+    'log_name': job_name,
+    'pbsworkdir': os.getcwd(),
+    'cmd': f'python3.6 {os.path.join(os.getcwd(), job_name + ".py")}',
+    'email': 'n/a'
+}
+
+# Save the updated configuration to a YAML file
+config_file_path = project_manager.user_log / Path("upload_config.yml")
+with open(str(config_file_path), 'w') as config_file:
+    yaml.dump(db_config, config_file, default_flow_style=False)
 
-# Set up database dispatcher and dispatch the functions
-dd = DatabaseDispatcher(config_file, pm)
-dd.dispatch(dd.strategies, dd.dispatcher, dd.configuration)
+# Initialize database dispatcher and execute dispatch functions
+db_dispatcher = DatabaseDispatcher(config_file_path, project_manager)
+db_dispatcher.dispatch(db_dispatcher.strategies, db_dispatcher.dispatcher, db_dispatcher.configuration)

OrthoEvol/Orthologs/Phylogenetics/PAML/README.md

@@ -1,36 +1,40 @@
 # PAML Documentation
+
 PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of
 programs for phylogenetic analyses of DNA or protein
 sequences using maximum likelihood and is maintained by Ziheng Yang.
 
 
 ## Why ETE?
-ETE is python package for building, comparing, annotating, manipulating and visualising
-trees. It provides a comprehensive API and a collection of command line tools,
- including utilities to work with the NCBI taxonomy tree.
+
+ETE is a python package for building, comparing, annotating, manipulating and visualising
+trees. It provides a comprehensive API and a collection of command line tools including 
+utilities to work with the NCBI taxonomy tree.
 
 ### Model Selection and Default Parameters
+
 It's important to note the default parameters for `ETE3PAML` are as follows:
-`model='M1'`, `workdir=```.
+`model='M1'`, `workdir=''`.
 
 ## Usage & Examples
 
 ### A simple implementation of ETE3PAML
+
 ```python
 from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML
 
-paml = ETE3PAML(alignmentfile='.ffn', speciestree='.nw', workdir='')
-
-paml.run(pamlsrc='path/to/codeml/binary', output_folder=None)
+paml = ETE3PAML(alignmentfile='.ffn', speciestree='tree.nw', workdir='', 
+                pamlsrc='path/to/codeml/binary')
 
+paml.run(output_folder=None)
 ```
 
 ### Pruning a tree for use with ETE3PAML
 
 ```python
 from OrthoEvol.Orthologs.Phylogenetics.PAML import ETE3PAML
 
-paml = ETE3PAML(alignmentfile='HTR1A.ffn', speciestree='speciestree.nw', workdir='')
+paml = ETE3PAML(infile='HTR1A.ffn', species_tree='speciestree.nw', workdir='')
 
 # Input a list of orgnanisms or an organisms csv file with header as 'Organisms'
 paml.prune_tree(organisms='organisms.csv')