update scripts for distribution

README.md

@@ -47,6 +47,7 @@ If you don't have poetry, you can simply run `pip install -r <>` for any of the
 ## Distributing
 * Use `poetry build` and `poetry publish`. Refer to [poetry docs](https://python-poetry.org/docs/)
 for more detail.
+* To re-generate the `requirements*.txt`, run `scripts/gen_requirements.py`.
 
 ### Bundling an Executable with PyInstaller
 **NOTE: This section is obsolete for now, as we are currently distributing with pip.**

pyproject.toml

@@ -18,7 +18,7 @@ marshmallow-polyfield = "^5.10"
 tellurium = { version = "^2.2.0", optional = true }
 sbml2matlab = { version = "1.2.3", optional = true }
 networkx = { version = "^2.5.1", optional = true }
-simplesbml = { git = "https://github.com/evilnose/simplesbml.git", branch = "master", optional = true }
+simplesbml = { git = "https://github.com/evilnose/simplesbml.git", rev = "dfd61aea", optional = true }
 python-libsbml = { version = "^5.18.0", optional = true }
 
 [tool.poetry.dev-dependencies]
@@ -38,3 +38,4 @@ coyote = 'rkviewer.main:main'
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+

requirements-dev.txt

@@ -10,9 +10,9 @@ autopep8==1.5.7 \
 babel==2.9.1; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" \
     --hash=sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9 \
     --hash=sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0
-certifi==2020.12.5; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5" \
-    --hash=sha256:719a74fb9e33b9bd44cc7f3a8d94bc35e4049deebe19ba7d8e108280cfd59830 \
-    --hash=sha256:1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c
+certifi==2021.5.30; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5" \
+    --hash=sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8 \
+    --hash=sha256:2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee
 chardet==4.0.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5" \
     --hash=sha256:f864054d66fd9118f2e67044ac8981a54775ec5b67aed0441892edb553d21da5 \
     --hash=sha256:0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa
@@ -33,9 +33,9 @@ idna==2.10; python_version >= "3.5" and python_full_version < "3.0.0" or python_
 imagesize==1.2.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" \
     --hash=sha256:6965f19a6a2039c7d48bca7dba2473069ff854c36ae6f19d2cde309d998228a1 \
     --hash=sha256:b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1
-importlib-metadata==4.0.1; python_version < "3.8" and python_version >= "3.6" \
-    --hash=sha256:d7eb1dea6d6a6086f8be21784cc9e3bcfa55872b52309bc5fad53a8ea444465d \
-    --hash=sha256:8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581
+importlib-metadata==4.4.0; python_version < "3.8" and python_version >= "3.6" \
+    --hash=sha256:960d52ba7c21377c990412aca380bf3642d734c2eaab78a2c39319f67c6a5786 \
+    --hash=sha256:e592faad8de1bda9fe920cf41e15261e7131bcf266c30306eec00e8e225c1dd5
 isort==5.8.0; python_version >= "3.6" and python_version < "4.0" \
     --hash=sha256:2bb1680aad211e3c9944dbce1d4ba09a989f04e238296c87fe2139faa26d655d \
     --hash=sha256:0a943902919f65c5684ac4e0154b1ad4fac6dcaa5d9f3426b732f1c8b5419be6
@@ -189,9 +189,9 @@ pycodestyle==2.7.0; python_version >= "2.7" and python_full_version < "3.0.0" or
 pygments==2.9.0; python_version >= "3.5" \
     --hash=sha256:d66e804411278594d764fc69ec36ec13d9ae9147193a1740cd34d272ca383b8e \
     --hash=sha256:a18f47b506a429f6f4b9df81bb02beab9ca21d0a5fee38ed15aef65f0545519f
-pylint==2.8.2; python_version >= "3.6" and python_version < "4.0" \
-    --hash=sha256:f7e2072654a6b6afdf5e2fb38147d3e2d2d43c89f648637baab63e026481279b \
-    --hash=sha256:586d8fa9b1891f4b725f587ef267abe2a1bad89d6b184520c7f07a253dd6e217
+pylint==2.8.3; python_version >= "3.6" and python_version < "4.0" \
+    --hash=sha256:792b38ff30903884e4a9eab814ee3523731abd3c463f3ba48d7b627e87013484 \
+    --hash=sha256:0a049c5d47b629d9070c3932d13bff482b12119b6a241a93bc460b0be16953c8
 pyparsing==2.4.7; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5" \
     --hash=sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b \
     --hash=sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1
@@ -225,18 +225,18 @@ sphinxcontrib-applehelp==1.0.2; python_version >= "3.5" \
 sphinxcontrib-devhelp==1.0.2; python_version >= "3.5" \
     --hash=sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4 \
     --hash=sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e
-sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5" \
-    --hash=sha256:e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b \
-    --hash=sha256:3c0bc24a2c41e340ac37c85ced6dafc879ab485c095b1d65d2461ac2f7cca86f
+sphinxcontrib-htmlhelp==2.0.0; python_version >= "3.6" \
+    --hash=sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2 \
+    --hash=sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07
 sphinxcontrib-jsmath==1.0.1; python_version >= "3.5" \
     --hash=sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8 \
     --hash=sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178
 sphinxcontrib-qthelp==1.0.3; python_version >= "3.5" \
     --hash=sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72 \
     --hash=sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6
-sphinxcontrib-serializinghtml==1.1.4; python_version >= "3.5" \
-    --hash=sha256:eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc \
-    --hash=sha256:f242a81d423f59617a8e5cf16f5d4d74e28ee9a66f9e5b637a18082991db5a9a
+sphinxcontrib-serializinghtml==1.1.5; python_version >= "3.5" \
+    --hash=sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952 \
+    --hash=sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd
 toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.3.0" \
     --hash=sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b \
     --hash=sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f
@@ -278,9 +278,9 @@ typing-extensions==3.10.0.0; python_version < "3.8" and python_version >= "3.6"
     --hash=sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497 \
     --hash=sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84 \
     --hash=sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342
-urllib3==1.26.4; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.5" \
-    --hash=sha256:2f4da4594db7e1e110a944bb1b551fdf4e6c136ad42e4234131391e21eb5b0df \
-    --hash=sha256:e7b021f7241115872f92f43c6508082facffbd1c048e3c6e2bb9c2a157e28937
+urllib3==1.26.5; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.5" \
+    --hash=sha256:753a0374df26658f99d826cfe40394a686d05985786d946fbe4165b5148f5a7c \
+    --hash=sha256:a7acd0977125325f516bda9735fa7142b909a8d01e8b2e4c8108d0984e6e0098
 wrapt==1.12.1; python_version >= "3.6" and python_version < "4.0" \
     --hash=sha256:b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7
 wxpython==4.1.1 \