Migrate code to be a package

.gitignore

@@ -2,8 +2,8 @@
 **/.directory
 */*.pyc
 .idea
-srv/database.sqlite
+dgenies/database.sqlite
 application.properties
 logs/*
 !logs/README
-srv/.local_scheduler_pid
+dgenies/.local_scheduler_pid

MANIFEST.in

+include dgenies/templates/*.html

application.properties.example

@@ -55,7 +55,7 @@ minimap2_cluster = ###DEFAULT###
 
 [database]
 type = sqlite
-url = ###PROGRAM###/srv/database.sqlite
+url = ###USER###/.dgenies/database.sqlite
 # Not used for sqlite:
 port =
 db =

bin

+src/dgenies/bin
\ No newline at end of file

bin/config_reader.py

-../srv/config_reader.py
\ No newline at end of file

lib

+src/dgenies/lib
\ No newline at end of file

logs

+src/dgenies/logs
\ No newline at end of file

setup.py

+from setuptools import setup, find_packages
+from pip.req import parse_requirements
+
+install_reqs = parse_requirements('requirements.txt', session='hack')
+# reqs is a list of requirement
+# e.g. ['django==1.5.1', 'mezzanine==1.4.6']
+reqs = [str(ir.req) for ir in install_reqs]
+
+setup(
+    name='dgenies',
+    version='0.9',
+    packages=find_packages('src'),
+    package_dir={'dgenies': 'src/dgenies'},
+    include_package_data=True,
+    zip_safe=False,
+    install_requires=reqs,
+    data_files=[('/etc/dgenies', {'application.properties':'application.properties.example'})]
+)

setup.py.bk

+from setuptools import setup, find_packages
+from pip.req import parse_requirements
+
+install_reqs = parse_requirements('requirements.txt', session='hack')
+# reqs is a list of requirement
+# e.g. ['django==1.5.1', 'mezzanine==1.4.6']
+reqs = [str(ir.req) for ir in install_reqs]
+
+setup(
+    name='dgenies',
+    version='0.9',
+    packages=find_packages('src'),
+    package_dir={'dgenies': 'src/dgenies'},
+    include_package_data=True,
+    zip_safe=False,
+    install_requires=reqs,
+    package_data={"dgenies": ["bin/*.py", "static/*/*.css", "static/*/*.js", "templates/*.html"]},
+    data_files=[('/etc/dgenies', {'application.properties':'application.properties.example'})]
+)

src/MANIFEST.in

+include dgenies/templates/*.html

src/dgenies/.local_scheduler_pid

+11206

src/dgenies/__init__.py

+#!/usr/bin/env python3
+
+import os
+from flask import Flask
+from .config_reader import AppConfigReader
+from .lib.mailer import Mailer
+from .lib.crons import Crons
+
+import sys
+
+app_folder = os.path.dirname(os.path.realpath(__file__))
+sys.path.insert(0, app_folder)
+os.environ["PATH"] = os.path.join(app_folder, "bin") + ":" + os.environ["PATH"]
+
+sqlite_file = os.path.join(app_folder, "database.sqlite")
+
+
+# Init config reader:
+config_reader = AppConfigReader()
+
+UPLOAD_FOLDER = config_reader.upload_folder
+APP_DATA = config_reader.app_data
+
+app_title = "D-GENIES - Dotplot for Genomes Interactive, E-connected and Speedy"
+
+# Init Flask:
+app = Flask(__name__, static_url_path='/static')
+app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
+app.config['MAX_CONTENT_LENGTH'] = config_reader.max_upload_file_size
+app.config['SECRET_KEY'] = 'dsqdsq-255sdA-fHfg52-25Asd5'
+
+# Init mail:
+mailer = Mailer(app)
+
+if config_reader.debug and config_reader.log_dir != "stdout" and not os.path.exists(config_reader.log_dir):
+    os.makedirs(config_reader.log_dir)
+
+# Crons:
+if os.getenv('DISABLE_CRONS') != "True":
+    print("Starting crons...")
+    crons = Crons(app_folder)
+    crons.start_all()
+
+from dgenies import views
+
+if __name__ == '__main__':
+    app.run()

bin/clean_jobs.py → src/dgenies/bin/clean_jobs.py

@@ -8,7 +8,7 @@ from _datetime import datetime, timedelta
 import traceback
 import argparse
 
-app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "srv")
+app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "dgenies")
 sys.path.insert(0, app_folder)
 
 from config_reader import AppConfigReader

bin/clear_crons.py → src/dgenies/bin/clear_crons.py

@@ -3,7 +3,7 @@
 import os
 from lib.crons import Crons
 
-app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "srv")
+app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "dgenies")
 
 crons = Crons(app_folder)
 crons.clear()

bin/clear_logs.py → src/dgenies/bin/clear_logs.py

@@ -4,7 +4,7 @@ import os
 import sys
 from glob import glob
 
-app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "srv")
+app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "dgenies")
 sys.path.insert(0, app_folder)
 
 from config_reader import AppConfigReader

src/dgenies/bin/config_reader.py

+../config_reader.py
\ No newline at end of file

bin/launch_server.sh → src/dgenies/bin/launch_server.sh

@@ -83,4 +83,4 @@ if [ "$LOCAL" == "True" ]; then
     host="127.0.0.1"
 fi
 
-DISABLE_CRONS=${DISABLE_CRONS} FLASK_DEBUG=${debug} FLASK_APP=${SCRIPTPATH}/../srv/main.py flask run --host=${host} --port=${PORT}
+DISABLE_CRONS=${DISABLE_CRONS} FLASK_DEBUG=${debug} FLASK_APP=dgenies flask run --host=${host} --port=${PORT}

bin/local_scheduler.py → src/dgenies/bin/local_scheduler.py

@@ -12,7 +12,7 @@ import argparse
 # Allow only one instance:
 me = singleton.SingleInstance()
 
-app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "srv")
+app_folder = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), "dgenies")
 os.environ["PATH"] = os.path.join(app_folder, "bin") + ":" + os.environ["PATH"]
 sys.path.insert(0, app_folder)