Parsing improvements - merge improve-parsing into master

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

@@ -12,19 +12,20 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: 3.11
     - 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 install -y python=3.11
         conda env update --file conda/environment.yml --name base
     - name: Test with pytest
       run: |
         conda install pytest pytest-cov
-        pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml --ignore='Testing/test_formal_methods.py'
+        pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml --ignore='Testing/test_formal_methods.py' --ignore='Testing/parsing/test_remote_parsing.py'

.readthedocs.yaml

@@ -5,12 +5,17 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
   configuration: docs/source/conf.py
 
 python:
-  version: "3.8"
   install:
     - requirements: docs/requirements.txt

Testing/models/get_model_str.py

@@ -0,0 +1,15 @@
+import os
+
+def get_model_str(model_name: str) -> str:
+    if not os.path.splitext(model_name)[1]:
+        model_name += ".txt"
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    file_path = os.path.join(script_dir, model_name)
+
+    try:
+        with open(file_path, "r") as file:
+            model_str = file.read()
+        return model_str
+    except FileNotFoundError:
+        print(f"File {file_path} not found")
+        return None

Testing/models/model1.txt

@@ -0,0 +1,12 @@
+#! rules
+X()::rep => @ k1*[X()::rep]
+Z()::rep => X()::rep
+=> Y()::rep @ 1/(1+([X()::rep])**4)
+
+#! inits
+2 X()::rep
+Y()::rep
+
+#! definitions
+k1 = 0.05
+k2 = 0.12 

Testing/models/model2.txt

@@ -0,0 +1,12 @@
+#! rules
+X(K{i})::rep => X(K{p})::rep @ k1*[X()::rep]
+X(T{a})::rep => X(T{o})::rep @ k2*[Z()::rep]
+=> Y(P{f})::rep @ 1/(1+([X()::rep])**4)
+
+#! inits
+2 X(K{c}, T{e}).X(K{c}, T{j})::rep
+Y(P{g}, N{l})::rep
+
+#! definitions
+k1 = 0.05
+k2 = 0.12

Testing/models/model3.txt

@@ -0,0 +1,12 @@
+#! rules
+Y{i}::rep => Y{a}::rep @ p*[Y{i}::rep]
+Y{i}::rep => Y{-}::rep @ (1-p)*[Y{i}::rep]
+X()::rep + Y{a}::rep => X().Y{a}::rep @ q*[X()::rep]*[Y{a}::rep]
+X(K{i}).Y{_}::rep => X(K{p}).Y{_}::rep @ p*[X(K{i}).Y{_}::rep] // also here
+
+#! inits
+2 X(K{i})::rep
+1 Y{i}::rep
+
+#! definitions
+p = 0.3

Testing/models/model4.txt

@@ -0,0 +1,11 @@
+#! rules
+X()::rep => @ k1*[X()::rep]
+Z()::rep => X()::rep @ k2
+=> Y()::rep @ 1/(1+([X()::rep])**4)
+
+#! inits
+2 X()::rep
+Y()::rep
+
+#! definitions
+k2 = 5

Testing/models/model5.txt

@@ -0,0 +1,12 @@
+#! rules
+// commenting
+X(K{i})::rep => X(K{p})::rep @ k1*[X()::rep] // also here
+X(T{a})::rep => X(T{o})::rep @ k2*[Z()::rep]
+=> Y(P{f})::rep @ 1/(1+([X()::rep])**4) // ** means power (^)
+
+#! inits
+2 X(K{c}, T{e})::rep
+Y(P{g}, N{l})::rep
+
+#! definitions
+k2 = 0.05 // also comment

Testing/models/model6.txt

@@ -0,0 +1,12 @@
+#! rules
+X()::rep => @ k1*[X()::rep]
+Z()::rep => X()::rep @ k2
+=> Y()::rep @ 1/(1+([X()::rep])**4)
+
+#! inits
+2 X()::rep
+Y()::rep
+
+#! definitions
+k2 = 5
+k1 = 2

Testing/models/model7.txt

@@ -0,0 +1,13 @@
+#! rules
+// commenting
+X(K{i})::rep => X(K{p})::rep @ k1*[X()::rep] // also here
+X(T{a})::rep => X(T{o})::rep @ k2*[Z()::rep]
+=> Y(P{f})::rep @ 1/(1+([X()::rep])**4) // ** means power (^)
+
+#! inits
+2 X(K{c}, T{e}).X(K{c}, T{j})::rep
+Y(P{g}, N{l})::rep
+
+#! definitions
+k2 = 0.05 // also comment
+k1 = 2

Testing/models/model_TS.txt

@@ -0,0 +1,15 @@
+#! rules
+=> K(S{u},T{i})::cyt @ omega
+K(S{u})::cyt => K(S{p})::cyt @ alpha*[K(S{u})::cyt]
+K(S{p})::cyt + B{a}::cyt => K(S{p}).B{a}::cyt @ beta*[K(S{p})::cyt]*[B{a}::cyt]
+B{_}::cyt => @ gamma*[B{_}::cyt]
+K(S{u},T{i}).B{a}::cyt => @ 5
+
+#! inits
+1 B{a}::cyt
+
+#! definitions
+alpha = 10
+beta = 5
+gamma = 2
+omega = 3

Testing/models/model_abstract.txt

@@ -0,0 +1,10 @@
+#! rules
+=> X()::rep @ k2*[T{_}::rep]
+T{a}::rep => T{i}::rep @ k1*[T{_}::rep]
+
+#! inits
+10 T{a}::rep
+
+#! definitions
+k1 = 0.05
+k2 = 0.12

Testing/models/model_bigger_TS.txt

@@ -0,0 +1,15 @@
+#! rules
+=> 2 K(S{u},T{i})::cyt @ omega
+K(S{u})::cyt => K(S{p})::cyt @ alpha*[K(S{u})::cyt]
+K(S{p})::cyt + B{a}::cyt => K(S{p}).B{a}::cyt @ beta*[K(S{p})::cyt]*[B{a}::cyt]
+B{_}::cyt => @ gamma*[B{_}::cyt]
+K(S{u},T{i}).B{a}::cyt => @ 5
+
+#! inits
+6 B{a}::cyt
+
+#! definitions
+alpha = 10
+beta = 5
+gamma = 2
+omega = 3

Testing/models/model_cmplx_in_abstr_seq1.txt

@@ -0,0 +1,5 @@
+#! rules
+S{i}::A()::A2::cell  => A()::cell
+
+#! complexes
+A2 = A().A()

Testing/models/model_cmplx_in_abstr_seq2.txt

@@ -0,0 +1,2 @@
+#! rules
+S{i}::A()::A().A()::cell => A()::cell

Testing/models/model_even_bigger_TS.txt

@@ -0,0 +1,15 @@
+#! rules
+=> K(S{u},T{i})::cyt @ omega
+K(S{u})::cyt => K(S{p})::cyt @ alpha*[K(S{u})::cyt]
+K(S{p})::cyt + B{a}::cyt => K(S{p}).B{a}::cyt @ beta*[K(S{p})::cyt]*[B{a}::cyt]
+B{_}::cyt => @ gamma*[B{_}::cyt]
+K(S{u},T{i}).B{a}::cyt => @ 5
+
+#! inits
+10 B{a}::cyt
+
+#! definitions
+alpha = 10
+beta = 5
+gamma = 2
+omega = 3

Testing/models/model_for_bound.txt

@@ -0,0 +1,9 @@
+#! rules
+=> A{i}::cyt @ k
+=> C{i}::cyt @ k
+
+#! inits
+2 B{i}::cyt
+
+#! definitions
+k = 1

Testing/models/model_for_matching.txt

@@ -0,0 +1,16 @@
+#! rules
+K(S{i}).B()::cyt + C{_}::cell => K(S{i})::cyt + B()::cyt + C{_}::cell @ 3*[K(S{i}).B()::cyt]/2*v_1
+A{p}.K(S{i})::cyt => A{i}::cyt + K(S{a})::cyt + C{a}::cyt @ 0.3*[A{p}.K(S{i})::cyt]
+K(S{i},T{i})::cyt + C{_}::cell => K(S{a},T{i})::cyt @ k2*[K(S{i},T{i})::cyt]
+C{_}::cell + C{_}::cell => C{_}.C{_}::cell @ v_1*[C{_}::cell]**2
+C{_}::cell + K()::cell => C{_}.K()::cell @ v_1*[C{_}::cell]**2
+
+#! inits
+2 K(S{i},T{i}).B(T{a})::cyt
+1 A{p}.K(S{i},T{i})::cyt
+2 C{i}::cell
+1 C{a}::cell
+
+#! definitions
+v_1 = 0.05
+k2 = 0.12

Testing/models/model_miyoshi.txt

@@ -0,0 +1,28 @@
+#! rules
+S{u}::KaiC()::KaiC6::cyt => S{p}::KaiC()::KaiC6::cyt @ (kcat1*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+S{p}::KaiC()::KaiC6::cyt => S{u}::KaiC()::KaiC6::cyt @ (kcat2*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{u}::KaiC()::KaiC6::cyt => T{p}::KaiC()::KaiC6::cyt @ (kcat3*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{p}::KaiC()::KaiC6::cyt => T{u}::KaiC()::KaiC6::cyt @ (kcat4*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+KaiB4{i}::cyt => KaiB4{a}::cyt @ (kcatb2*[KaiB4{i}::cyt])/(Kmb2 + [KaiB4{i}::cyt])
+KaiB4{a}::cyt => KaiB4{i}::cyt @ (kcatb1*[KaiB4{a}::cyt])/(Kmb1 + [KaiB4{a}::cyt])
+KaiB4{a}.KaiA2()::cyt => KaiB4{a}::cyt + KaiA2()::cyt @ k12*[KaiB4{a}.KaiA2()::cyt]
+KaiC6::cyt => 6 KaiC()::cyt @ kdimer*[KaiC6::cyt]
+6 KaiC()::cyt => KaiC6::cyt @ kdimer*[KaiC()::cyt]*([KaiC()::cyt] - 1)*([KaiC()::cyt] - 2)*([KaiC()::cyt] - 3)*([KaiC()::cyt] - 4)*([KaiC()::cyt] - 5)
+
+#! inits
+6 KaiC(S{p},T{p})::cyt
+1 KaiB4{a}.KaiA2()::cyt
+
+#! definitions
+kcat1 = 0.539
+kcat3 = 0.89
+Km = 0.602
+kcatb2 = 0.346
+kcatb1 = 0.602
+Kmb2 = 66.75
+Kmb1 = 2.423
+k12 = 0.0008756
+kdimer = 1.77
+
+#! complexes
+KaiC6 = KaiC().KaiC().KaiC().KaiC().KaiC().KaiC()

Testing/models/model_miyoshi_non_param.txt

@@ -0,0 +1,33 @@
+#! rules
+S{u}:KaiC():KaiC6::cyt => S{p}:KaiC():KaiC6::cyt @ (kcat1*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+S{p}:KaiC():KaiC6::cyt => S{u}:KaiC():KaiC6::cyt @ (kcat2*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{u}:KaiC():KaiC6::cyt => T{p}:KaiC():KaiC6::cyt @ (kcat3*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{p}:KaiC():KaiC6::cyt => T{u}:KaiC():KaiC6::cyt @ (kcat4*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+KaiB4{i}::cyt => KaiB4{a}::cyt @ (kcatb2*[KaiB4{i}::cyt])/(Kmb2 + [KaiB4{i}::cyt])
+KaiB4{a}::cyt => KaiB4{i}::cyt @ (kcatb1*[KaiB4{a}::cyt])/(Kmb1 + [KaiB4{a}::cyt])
+KaiB4{a}.KaiA2()::cyt => KaiB4{a}::cyt + KaiA2()::cyt @ k12*[KaiB4{a}.KaiA2()::cyt]
+KaiC6::cyt => 6 KaiC()::cyt @ kdimer*[KaiC6::cyt]
+6 KaiC()::cyt => KaiC6::cyt @ kdimer*[KaiC()::cyt]
+KaiC().KaiC()::cyt => KaiC()::cyt + KaiC()::cyt @ kcat1
+
+#! inits
+6 KaiC(S{p},T{p})::cyt
+1 KaiB4{a}.KaiA2()::cyt
+1 KaiC(S{u},T{p})::cyt
+1 KaiC(S{u},T{p}).KaiC(S{p},T{p})::cyt
+
+#! definitions
+kcat2 = 0.539
+kcat4 = 0.89
+kcat1 = 0.539
+kcat3 = 0.89
+Km = 0.602
+kcatb2 = 0.346
+kcatb1 = 0.602
+Kmb2 = 66.75
+Kmb1 = 2.423
+k12 = 0.0008756
+kdimer = 1.77
+
+#! complexes
+KaiC6 = KaiC().KaiC().KaiC().KaiC().KaiC().KaiC()

Testing/models/model_nonreachable.txt

@@ -0,0 +1,11 @@
+#! rules
+K(S{i}).B()::cyt => K(S{a})::cyt + B()::cyt @ 3*[K(S{i}).B()::cyt]/2*v_1
+K(S{a})::cyt + A{i}::cyt => K(S{a}).A{i}::cyt
+
+#! inits
+2 K(S{i}).B()::cyt
+1 A{i}::cyt
+
+#! definitions
+v_1 = 0.05
+k2 = 0.12

Testing/models/model_parametrised.txt

@@ -0,0 +1,12 @@
+#! rules
+// commenting
+X(K{i})::rep => X(K{p})::rep @ k1*[X()::rep] // also here
+X(T{a})::rep => X(T{o})::rep @ k2*[Z()::rep]
+=> Y(P{f})::rep @ 1/(v_3+([X()::rep])**4) // ** means power (^)
+
+#! inits
+2 X(K{c}, T{e}).X(K{c}, T{j})::rep
+Y(P{g}, N{l})::rep // comment just 1 item
+
+#! definitions
+k1 = 0.05

Testing/models/model_parametrised2.txt

@@ -0,0 +1,15 @@
+#! rules
+=> K(S{u},T{i})::cyt @ omega
+K(S{u})::cyt => K(S{p})::cyt @ alpha*[K(S{u})::cyt]
+K(S{p})::cyt + B{a}::cyt => K(S{p}).B{a}::cyt @ beta*[K(S{p})::cyt]*[B{a}::cyt]
+B{_}::cyt => @ gamma*[B{_}::cyt]
+K(S{u},T{i}).B{a}::cyt => @ 5
+
+#! inits
+1 B{a}::cyt
+
+#! definitions
+alpha = 10
+beta = 5
+//gamma = 2
+omega = 3

Testing/models/model_reachable.txt

@@ -0,0 +1,12 @@
+#! rules
+K(S{i}).B()::cyt => K(S{a})::cyt + B()::cyt @ 3*[K(S{i}).B()::cyt]/2*v_1
+K(S{a})::cyt + A{i}::cyt => K(S{a}).A{i}::cyt
+K().A{i}::cyt => K().A{a}::cyt
+
+#! inits
+2 K(S{i}).B()::cyt
+1 A{i}::cyt
+
+#! definitions
+v_1 = 0.05
+k2 = 0.12

Testing/models/model_with_comments.txt

@@ -0,0 +1,15 @@
+#! rules
+// commenting
+X(K{i})::rep => X(K{p})::rep @ k1*[X()::rep] // also here
+X(T{a})::rep => X(T{o})::rep @ k2*[Z()::rep]
+=> Y(P{f})::rep @ 1/(1+([X()::rep])**4) // ** means power (^)
+
+#! inits
+// here
+2 X(K{c}, T{e}).X(K{c}, T{j})::rep
+Y(P{g}, N{l})::rep // comment just 1 item
+
+#! definitions
+// and
+k1 = 0.05 // also
+k2 = 0.12