Added separate section for ODE in requirements and update setup to ac…

…count for ODE

.github/workflows/test-install.yml

@@ -11,6 +11,7 @@ env:
   INSTALLLPY: 0
   INSTALLMATLAB: 0
   INSTALLMPI: 1
+  INSTALLODE: 1
   INSTALLOMP: 1
   INSTALLPYGMENTS: 1
   INSTALLPYTORCH: 1

recipe/meta.yaml

@@ -57,7 +57,6 @@ requirements:
     - sysv_ipc  # [not win]
   run:
     - GitPython
-    - antlr-python-runtime ==4.10
     - chevron
     - deprecation
     - flask
@@ -73,7 +72,6 @@ requirements:
     - requests
     - scipy
     - six
-    - sympy >=1.10
     - sysv_ipc  # [not win]
     - toml
     - unyt
@@ -238,6 +236,18 @@ outputs:
         - {{ pin_subpackage('yggdrasil', exact=True) }}
         - openpyxl
         - pandas
+  - name: yggdrasil.ode
+    build:
+      string: py{{ PY_VER_MAJOR }}{{ PY_VER_MINOR }}h{{ PKG_HASH }}_{{ PKG_BUILDNUM }}
+      run_exports:
+        - {{ pin_subpackage('yggdrasil.ode') }}
+    requirements:
+      host:
+        - python
+      run:
+        - {{ pin_subpackage('yggdrasil', exact=True) }}
+        - antlr-python-runtime ==4.10
+        - sympy >=1.10
   - name: yggdrasil.testing
     build:
       string: py{{ PY_VER_MAJOR }}{{ PY_VER_MINOR }}h{{ PKG_HASH }}_{{ PKG_BUILDNUM }}

requirements.txt

@@ -1,5 +1,4 @@
 GitPython
-antlr4-python3-runtime==4.10  # [pip]
 chevron
 deprecation
 flask
@@ -13,7 +12,6 @@ pyzmq
 requests
 scipy
 six
-sympy>=1.10
 sysv_ipc; platform_system != 'Windows'
 toml
 unyt

utils/requirements/requirements.json

@@ -94,7 +94,6 @@
       }
     },
     "six",
-    "sympy>=1.10",
     "toml",
     "unyt",
     "GitPython",
@@ -103,18 +102,6 @@
         "os": "unix",
         "host": true
       }
-    },
-    {
-      "antlr": [
-        {
-          "name": "antlr4-python3-runtime==4.10",
-          "method": "pip"
-        },
-        {
-          "name": "antlr-python-runtime==4.10",
-          "method": "conda"
-        }
-      ]
     }
   ],
   "extras": {
@@ -603,6 +590,24 @@
         "openpyxl"
       ]
     },
+    "ode": {
+      "description": "Dependencies required to run symbolic ODE models",
+      "requirements": [
+        {
+          "antlr": [
+            {
+              "name": "antlr4-python3-runtime==4.10",
+              "method": "pip"
+            },
+            {
+              "name": "antlr-python-runtime==4.10",
+              "method": "conda"
+            }
+          ]
+        },
+        "sympy>=1.10"
+      ]
+    },
     "testing": {
       "description": "Dependencies required to run yggdrasil tests",
       "requirements": [

utils/requirements/requirements.yaml

@@ -54,18 +54,12 @@ general:
       flags:
         method_in_setup: conda
   - six
-  - sympy>=1.10
   - toml
   - unyt
   - GitPython
   - sysv_ipc:
       os: unix
       host: True
-  - antlr:
-      - name: antlr4-python3-runtime==4.10
-        method: pip
-      - name: antlr-python-runtime==4.10
-        method: conda
 
 extras:
   c:
@@ -349,6 +343,15 @@ extras:
     requirements:
     - pandas
     - openpyxl
+  ode:
+    description: Dependencies required to run symbolic ODE models
+    requirements:
+    - antlr:
+      - name: antlr4-python3-runtime==4.10
+        method: pip
+      - name: antlr-python-runtime==4.10
+        method: conda
+    - sympy>=1.10
   testing:
     description: Dependencies required to run yggdrasil tests
     requirements:

utils/requirements/requirements_extras.json

@@ -23,6 +23,10 @@
     "openpyxl",
     "pandas"
   ],
+  "ode": [
+    "antlr4-python3-runtime==4.10",
+    "sympy>=1.10"
+  ],
   "testing": [
     "coverage",
     "flake8",

utils/requirements/requirements_optional.txt

@@ -6,4 +6,5 @@ pandas           # [excel]
 pika>=1.0.0      # [rmq]
 pillow           # [images]
 pygments         # [pygments]
+sympy>=1.10      # [ode]
 trimesh          # [trimesh]

utils/requirements/requirements_piponly.txt

@@ -1,3 +1,4 @@
+antlr4-python3-runtime==4.10  # [pip,ode]
 libroadrunner    # [pip,sbml]
 pysam; platform_system != 'Windows'  # [pip,seq]
 torch            # [pip,pytorch]

utils/setup_test_env.py

@@ -843,6 +843,7 @@ def get_install_opts(old=None, empty=False):
             'images': False,
             'seq': False,
             'excel': False,
+            'ode': False,
             'omp': False,
             'docs': False,
             'no_sudo': False,
@@ -868,6 +869,7 @@ def get_install_opts(old=None, empty=False):
             'images': (os.environ.get('INSTALLIMAGES', '0') == '1'),
             'seq': (os.environ.get('INSTALLSEQ', '0') == '1'),
             'excel': (os.environ.get('INSTALLEXCEL', '0') == '1'),
+            'ode': (os.environ.get('INSTALLODE', '0') == '1'),
             'omp': (os.environ.get('INSTALLOMP', '0') == '1'),
             'docs': (os.environ.get('BUILDDOCS', '0') == '1'),
             'no_sudo': False,
@@ -894,6 +896,7 @@ def get_install_opts(old=None, empty=False):
             'images': True,
             'seq': True,
             'excel': True,
+            'ode': True,
             'omp': False,
             'docs': True,
             'no_sudo': False,
@@ -920,6 +923,8 @@ def get_install_opts(old=None, empty=False):
             out.update(fortran=False, zmq=False)
         if out['docs']:
             out['r'] = True  # Allow roxygen
+    if sys.version_info[:2] < (3, 8):
+        out['ode'] = False  # sympy dropped support for Python < 3.8
     return out
 
 
@@ -1768,7 +1773,7 @@ def verify_pkg(install_opts=None):
     sys.stdout.flush()
     from yggdrasil.tools import is_lang_installed, is_comm_installed
     errors = []
-    for name in ['c', 'r', 'fortran', 'sbml', 'lpy', 'julia']:
+    for name in ['c', 'r', 'fortran', 'sbml', 'lpy', 'julia', 'ode']:
         flag = install_opts[name]
         if flag and (not is_lang_installed(name)):
             errors.append("Language '%s' should be installed, but is not."

utils/test-install-base.yml

@@ -26,6 +26,7 @@ env:
   INSTALLIMAGES: 1
   INSTALLSEQ: 1
   INSTALLEXCEL: 1
+  INSTALLODE: 1
   INSTALLOMP: 1
   INSTALLMPI: 1
   INSTALLMATLAB: 0