Modernize dependencies, tests, and Python support.

.github/workflows/ci.yml

@@ -2,17 +2,17 @@ name: Python CI
 
 on:
   push:
-    branches: [ master, main, dev-master, dev-refactored, refactor-phylo ]
+    branches: [ main, dev]
   pull_request:
-    branches: [ master, main, dev-master, dev-refactored, refactor-phylo ]
+    branches: [ main, dev]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -56,4 +56,4 @@ jobs:
 
     - name: Notify failure
       if: failure()
-      run: echo "Build failed"
+      run: echo "Build failed"

.github/workflows/docs.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
 
     - name: Cache pip
       uses: actions/cache@v4

OrthoEvol/Cookies/cookie_jar.py

@@ -7,18 +7,17 @@
 import yaml
 from cookiecutter.hooks import run_script
 from cookiecutter.main import cookiecutter
-from pkg_resources import resource_filename
-
 # OrthoEvol
 from OrthoEvol import Cookies
 from OrthoEvol.Manager.config import yml
+from OrthoEvol.resources import package_resource_path
 from OrthoEvol.Tools.logit import LogIt
 
 
 class CookBook(object):
     """Class of cookiecutter related functions."""
 
-    _config_file = resource_filename(yml.__name__, "cookie_recipes.yml")
+    _config_file = package_resource_path(yml, "cookie_recipes.yml")
 
     def __init__(self, config_file=_config_file, **new_recipes):
         """Access paths to the various cookiecutter templates.
@@ -28,7 +27,7 @@ def __init__(self, config_file=_config_file, **new_recipes):
 
         New Recipes can also be added...
         """
-        self.CookieJar = Path(resource_filename(Cookies.__name__, ''))
+        self.CookieJar = package_resource_path(Cookies)
         self.repo_cookie = self.CookieJar / Path('new_repository')
         self.user_cookie = self.CookieJar / Path('new_user')
         self.project_cookie = self.CookieJar / Path('new_project')

OrthoEvol/Cookies/new_website/{{cookiecutter.website_name}}/requirements/dev.txt

@@ -2,7 +2,7 @@
 -r prod.txt
 
 # Testing
-pytest==3.0.7
+pytest==9.1.1
 WebTest==2.0.27
 factory-boy==2.8.1
 

OrthoEvol/Cookies/new_website/{{cookiecutter.website_name}}/requirements/prod.txt

@@ -1,43 +1,40 @@
 # Everything needed in production
 
 # Flask
-Flask==2.2.5
-MarkupSafe==1.0
+Flask==3.1.3
+MarkupSafe==3.0.3
 Werkzeug==3.1.5
 Jinja2==3.1.6
 
-itsdangerous==0.24
-click>=5.0
+itsdangerous==2.2.0
+click==8.4.2
 
 # Database
-Flask-SQLAlchemy==2.2
-psycopg2==2.7.1
-SQLAlchemy==1.2.19
+Flask-SQLAlchemy==3.1.1
+psycopg2-binary==2.9.12
+SQLAlchemy==2.0.51
 
 # Migrations
-Flask-Migrate==2.0.3
+Flask-Migrate==4.1.0
 
 # Forms
-Flask-WTF==0.14.2
-WTForms==2.1
+Flask-WTF==1.3.0
+WTForms==3.2.2
 
 # Deployment
 gunicorn>=19.1.1
 
 # Assets
-Flask-Assets==0.12
+Flask-Assets==2.1.0
 cssmin>=0.2.0
 jsmin>=2.0.11
 
-# Admin
-Flask-User==0.6.11
-
 # Auth
-Flask-Login==0.4.0
-Flask-Bcrypt==0.7.1
+Flask-Login==0.6.3
+Flask-Bcrypt==1.0.1
 
 # Caching
 Flask-Caching>=1.0.0
 
 # Debug toolbar
-Flask-DebugToolbar==0.10.1
+Flask-DebugToolbar==0.16.0

OrthoEvol/Manager/biosql/biosql.py

@@ -1,7 +1,6 @@
 # Standard Library
 import os
 import subprocess as sp
-import pkg_resources
 from pathlib import Path
 # BioPython
 from BioSQL import BioSeqDatabase
@@ -12,6 +11,7 @@
 from OrthoEvol.Manager.management import ProjectManagement
 from OrthoEvol.Manager.biosql.biosql_repo import sql
 from OrthoEvol.Manager.biosql.biosql_repo import scripts as sql_scripts
+from OrthoEvol.resources import package_resource_path
 
 
 class BaseBioSQL(object):
@@ -46,9 +46,13 @@ def __init__(self, database_name, template_name="", project=None, project_path=N
         self.biosql_proc = self.biosql_utils.system_cmd
 
         # Load relative and absolute paths to scripts in the BioSQL module
-        self.scripts = pkg_resources.resource_filename(sql_scripts.__name__, "")
-        self.ncbi_taxon_script = pkg_resources.resource_filename(sql_scripts.__name__, "load_ncbi_taxonomy.pl")
-        self.itis_taxon_script = pkg_resources.resource_filename(sql_scripts.__name__, "load_itis_taxonomy.pl")
+        self.scripts = package_resource_path(sql_scripts)
+        self.ncbi_taxon_script = package_resource_path(
+            sql_scripts, "load_ncbi_taxonomy.pl"
+        )
+        self.itis_taxon_script = package_resource_path(
+            sql_scripts, "load_itis_taxonomy.pl"
+        )
         if database_name:
             self.database_name = Path(database_name)
 
@@ -132,7 +136,7 @@ def load_sqlite_schema(self):
         """
         # Build the command
         if not self.template_abs_path.is_file():
-            schema_file = pkg_resources.resource_filename(sql.__name__, self.schema_file)
+            schema_file = package_resource_path(sql, self.schema_file)
             schema_cmd = self.schema_cmd % str(self.template_abs_path)
             # Run the bash command
             self.configure_new_database(schema_cmd, schema_file)

OrthoEvol/Manager/config/templates/upload_rr_pbs.py

@@ -58,7 +58,6 @@ def _dispatch_config(config_file):
          "from OrthoEvol.Manager.management import ProjectManagement\n" \
          "from OrthoEvol.Manager.database_dispatcher import DatabaseDispatcher\n" \
          "from OrthoEvol.Manager.config import yml\n" \
-         "from pkg_resources import resource_filename\n" \
          "import yaml\n" \
          "pm_config_file = \"%%s\"\n" \
          "with open(pm_config_file, \'r\') as f:\n" \
@@ -87,4 +86,4 @@ def _dispatch_config(config_file):
 
 # Dispatch PBS jobs
 disp, conf = _dispatch_config(config_file)
-dd.dispatch(strategies=list(disp.keys()),dispatcher=disp, configuration=conf)
+dd.dispatch(strategies=list(disp.keys()),dispatcher=disp, configuration=conf)

OrthoEvol/Manager/data_management.py

@@ -1,14 +1,14 @@
 # Standard Library
-import pkg_resources
-import yaml
+import yaml
 # OrthoEvol
-from OrthoEvol.Manager.management import ProjectManagement
-from OrthoEvol.Manager import config
+from OrthoEvol.Manager.management import ProjectManagement
+from OrthoEvol.Manager.config import yml
 from OrthoEvol.Manager.database_management import BaseDatabaseManagement
 from OrthoEvol.Orthologs.Align import MultipleSequenceAlignment as MSA
 from OrthoEvol.Orthologs.Blast.blast import OrthoBlastN
 from OrthoEvol.Orthologs.Blast.comparative_genetics import BaseComparativeGenetics
-from OrthoEvol.Orthologs.GenBank.genbank import GenBank
+from OrthoEvol.Orthologs.GenBank.genbank import GenBank
+from OrthoEvol.resources import package_resource_path
 
 
 #import configparser
@@ -43,13 +43,13 @@ def __init__(self, config_file=None, pipeline=None, new=False, start=False, **kw
             self.GenBank_config = self.Alignment_config = None
         # Alignment configuration
         self.Guidance_config = self.Clustalo_config = self.Pal2Nal_config = None
-        self.pm = self.bl = self.gb = self.al = self.db = None
-        if pipeline == 'Ortho_CDS_1':
-            if new is True:
-                config_file = pkg_resources.resource_filename(config.yaml.__name__, 'pipeline.yml')
-            else:
-                config_file = pkg_resources.resource_filename(
-                    config.yaml.__name__, 'config_template_existing.yml')
+        self.pm = self.bl = self.gb = self.al = self.db = None
+        if pipeline == 'Ortho_CDS_1':
+            if new is True:
+                config_file = package_resource_path(yml, 'pipeline.yml')
+            else:
+                config_file = package_resource_path(
+                    yml, 'initialize_old.yml')
         if config_file is not None:
             if start is True:
                 self.configure(config_file)

OrthoEvol/Manager/database_management.py

@@ -8,7 +8,6 @@
 from collections import OrderedDict
 from importlib import import_module
 from pathlib import Path
-from pkg_resources import resource_filename
 import subprocess as sp
 # OrthoEvol
 from OrthoEvol import OrthoEvolDeprecationWarning
@@ -19,6 +18,7 @@
 from OrthoEvol.Manager.management import ProjectManagement
 from OrthoEvol.Orthologs.Blast.comparative_genetics import BaseComparativeGenetics
 from OrthoEvol.Manager.config import templates
+from OrthoEvol.resources import package_resource_path
 
 
 class BaseDatabaseManagement(object):
@@ -752,7 +752,7 @@ def NCBI_refseq_release(self, configure_flag=None, archive_flag=None, delete_fla
             db_path = self.database_path / Path('NCBI') / Path('refseq') / Path('release') / Path(collection_subset)
 
             # Read the upload script
-            upload_script = resource_filename(templates.__name__, 'upload_rr_pbs.py')
+            upload_script = package_resource_path(templates, 'upload_rr_pbs.py')
             with open(upload_script, 'r') as upload_script:
                 temp_script = upload_script.read()
             rand_str = random.sample(string.ascii_letters + string.digits, 5)

OrthoEvol/Manager/management.py

@@ -1,12 +1,12 @@
 """Directory management tools for the package."""
 # Standard Library
 import os
-from pathlib import Path
-import pkg_resources
-# OrthoEvol
-from OrthoEvol import Cookies, Orthologs, Manager, Tools
-from OrthoEvol.Cookies import Oven
-from OrthoEvol.Tools.logit import LogIt
+from pathlib import Path
+# OrthoEvol
+from OrthoEvol import Cookies, Orthologs, Manager, Tools
+from OrthoEvol.Cookies import Oven
+from OrthoEvol.resources import package_resource_path
+from OrthoEvol.Tools.logit import LogIt
 
 
 class Management(object):
@@ -37,19 +37,19 @@ def __init__(self, repo=None, home=os.getcwd(), new_repo=False, **kwargs):
         self.Kitchen = Oven(repo=self.repo, output_dir=self.file_home)
         self.Pantry = self.Kitchen.Recipes
         # Manager Module:
-        self.Manager = Path(pkg_resources.resource_filename(Manager.__name__, ''))
+        self.Manager = package_resource_path(Manager)
         self.BioSQL = self.Manager / Path('BioSQL')
         self.SQLite3 = self.BioSQL / Path('sqlite')
         self.MySQL = self.BioSQL / Path('mysql')
         self.config = self.Manager / Path('config')
         # Orthologs Module:
-        self.Orthologs = Path(pkg_resources.resource_filename(Orthologs.__name__, ''))
+        self.Orthologs = package_resource_path(Orthologs)
         self.Align = self.Orthologs / Path('Align')
         self.Blast = self.Orthologs / Path('Blast')
         self.GenBank = self.Orthologs / Path('GenBank')
         self.Phylogenetics = self.Orthologs / Path('Phylogenetics')
         # Tools Module:
-        self.Tools = Path(pkg_resources.resource_filename(Tools.__name__, ''))
+        self.Tools = package_resource_path(Tools)
         self.ftp = self.Tools / Path('ftp')
         self.logit = self.Tools / Path('logit')
         self.mpi = self.Tools / Path('mpi')

OrthoEvol/Manager/webster.py

@@ -1,10 +1,10 @@
 # Standard Library
 import re
 import textwrap as twrap
-from pathlib import Path
-from pkg_resources import resource_filename
-# OrthoEvol
-from OrthoEvol.Manager.config import references
+from pathlib import Path
+# OrthoEvol
+from OrthoEvol.Manager.config import references
+from OrthoEvol.resources import package_resource_path
 
 
 
@@ -39,16 +39,16 @@ class Webster(object):
                 Unreliable Alignment Regions Accounting for the Uncertainty of Multiple Parameters.  Nucleic Acids
                 Research, 2015 Jul 1; 43 (Web Server issue): W7-W14.; doi: 10.1093/nar/gkq443""",
                 "link": "https://www.ncbi.nlm.nih.gov/pubmed/18229673",
-                "path": resource_filename(
-                    references.__name__, "GUIDANCE2_Accurate_Detection_of_Unreliable_Alignment_Regions_Accounting_for_"
+                "path": package_resource_path(
+                    references, "GUIDANCE2_Accurate_Detection_of_Unreliable_Alignment_Regions_Accounting_for_"
                                          "the_Uncertainty_of_Multiple_Parameters.pdf")
             },
             "reference_2": {
                 "citation": u"""Landan, G., and D. Graur. (2008).  Local Reliability Measures from Sets of Co-optimal
                 Multiple Sequence Alignments.  Pac Symp Biocomput 13:15-24""",
                 "link": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489236/",
-                "path": resource_filename(
-                    references.__name__, "Local_Reliability_Measures_from_Sets_of_Co-optimal_Multiple_Sequence_"
+                "path": package_resource_path(
+                    references, "Local_Reliability_Measures_from_Sets_of_Co-optimal_Multiple_Sequence_"
                                          "Alignments.pdf")
             }
         },

OrthoEvol/Orthologs/Blast/comparative_genetics.py

@@ -5,13 +5,13 @@
 import time
 import copy
 import random
-import pkg_resources
 from pathlib import Path
 # OrthoEvol
 from OrthoEvol.Manager.config import data
 from OrthoEvol.Manager.management import ProjectManagement
 from OrthoEvol.utilities import FullUtilities
 from OrthoEvol.Tools.logit import LogIt
+from OrthoEvol.resources import package_resource_path
 # Other
 import pandas as pd
 from ete3 import NCBITaxa
@@ -125,7 +125,7 @@ def __init__(self, project=None, project_path=os.getcwd(), acc_file=None,
             self.taxon_path = self.project_index / Path(self.taxon_file)
         # Handle the master accession file (could be before or after blast)
         if kwargs["copy_from_package"]:
-            shutil.copy(pkg_resources.resource_filename(data.__name__, self.acc_file),
+            shutil.copy(package_resource_path(data, self.acc_file),
                         str(self.project_index))
         else:
             shutil.copy(self.acc_file, str(self.project_index))

OrthoEvol/Orthologs/Phylogenetics/PAML/codeml.py

@@ -2,11 +2,11 @@
 import os
 from pathlib import Path
 from shutil import copy
-import pkg_resources
-# BioPython
+# BioPython
 from Bio.Phylo.PAML import codeml
 # OrthoEvol
-from OrthoEvol.Manager.config import paml_control_files
+from OrthoEvol.Manager.config import paml_control_files
+from OrthoEvol.resources import package_resource_path
 
 
 class CodemlRun(object):
@@ -39,8 +39,8 @@ def __init__(self, P2N_alignment, iqtree_newick, control_file='codeml-8-11-2017.
         # Set up genes control file name and get the OrthoEvol control file path
         self.gene = str(iqtree_newick).replace('_iqtree.nwk', '')
         self.control_file = self.paml_path / Path(self.gene + '.ctl')
-        self.control_template = pkg_resources.resource_filename(
-            paml_control_files.__name__, control_file)
+        self.control_template = package_resource_path(
+            paml_control_files, control_file)
         print(self.control_template)
 
         # Set up CODEML input files

OrthoEvol/README.md

@@ -1,6 +1,6 @@
 Tutorial
 =============
-OrthoEvolution has been built with Python 3.9 (and up) as a multi-faceted package and pipeline
+OrthoEvolution has been built with Python 3.11 (and up) as a multi-faceted package and pipeline
 framework for comparative genetics in order to infer orthologous genes.
 
 Currently, this python package is comprised of 5 major modules: