From f05ea9ea635aae5737da448c80531c147372bc05 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Wed, 30 Oct 2024 12:19:28 -0600
Subject: [PATCH 01/20] more closely align linux/mac conda envs

---
 py3-opgee-linux.yml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/py3-opgee-linux.yml b/py3-opgee-linux.yml
index adfd0bf3..7050ab6d 100644
--- a/py3-opgee-linux.yml
+++ b/py3-opgee-linux.yml
@@ -10,12 +10,10 @@ dependencies:
   - dask
   - dask-jobqueue
   - graphviz
-  - python-graphviz
   - jinja2
   - llvm-openmp
   - lxml
   - networkx
-  - nuitka
   - numba
   - numpy
   - pandas
@@ -24,17 +22,18 @@ dependencies:
   - pip
   - pydot
   - pytest
+  - python-graphviz
   - python>=3.9.0,<3.10.0
   - semver
   - setuptools
-  - sphinx>=4.3.0
+  - sphinx
   - sphinx-argparse
-  - sphinx_rtd_theme>=0.5.1
+  - sphinx_rtd_theme
   - sphinxcontrib-serializinghtml
   - pip:
-    - dash-cytoscape==0.3.0
-    - pyXSteam==0.4.9
-    - thermosteam==0.34.0
+    - dash-cytoscape
+    - pyXSteam
+    - thermosteam
     - fluids==1.0.24
     - chemicals==1.1.4
     - thermo==0.2.25

From 305c9db2d4ae9f10210b21f2da562eff91a0a10c Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Wed, 30 Oct 2024 12:39:42 -0600
Subject: [PATCH 02/20] remove cython, update env export, add test step

---
 .github/workflows/opgee-test.yml | 4 +++-
 opgee-linux64.pkg_list.txt       | 6 +++---
 py3-opgee-linux.yml              | 1 -
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index b55cd719..933202ee 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -52,4 +52,6 @@ jobs:
         pip install -e .
         python -m pip install -e .
         pip install pytest-cov codecov coveralls PyYAML
-      if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.cache-hit != 'true'
\ No newline at end of file
+      if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.cache-hit != 'true'
+    - name: Run unit tests with coverage
+      run: coverage run --source=opgee -m pytest
diff --git a/opgee-linux64.pkg_list.txt b/opgee-linux64.pkg_list.txt
index b6162271..cd1c29f9 100644
--- a/opgee-linux64.pkg_list.txt
+++ b/opgee-linux64.pkg_list.txt
@@ -57,7 +57,7 @@ dask-jobqueue=0.8.2=py39h06a4308_0
 decorator=5.1.1=pypi_0
 distributed=2024.5.0=py39h06a4308_0
 docutils=0.18.1=py39h06a4308_3
-et-xmlfile=1.1.0=pypi_0
+et-xmlfile=2.0.0=pypi_0
 exceptiongroup=1.2.0=py39h06a4308_0
 executing=2.1.0=pypi_0
 expat=2.6.3=h6a678d5_0
@@ -165,7 +165,7 @@ nspr=4.35=h6a678d5_0
 nss=3.89.1=h6a678d5_0
 nuitka=1.5.8=py39h5eee18b_0
 numba=0.60.0=py39h6a678d5_0
-numexpr=2.8.7=py39h286c3b5_0
+numexpr=2.10.1=py39hd28fd6d_0
 numpy=1.26.4=py39heeff2f4_0
 numpy-base=1.26.4=py39h8a23956_0
 openjpeg=2.5.2=he7f1fd0_0
@@ -236,7 +236,7 @@ sqlite=3.45.3=h5eee18b_0
 stack-data=0.6.3=pypi_0
 tbb=2021.8.0=hdb19cb5_0
 tblib=1.7.0=pyhd3eb1b0_0
-tenacity=8.2.3=py39h06a4308_0
+tenacity=9.0.0=py39h06a4308_0
 thermo=0.2.25=pypi_0
 thermosteam=0.34.0=pypi_0
 tk=8.6.14=h39e8969_0
diff --git a/py3-opgee-linux.yml b/py3-opgee-linux.yml
index 7050ab6d..e22cdae1 100644
--- a/py3-opgee-linux.yml
+++ b/py3-opgee-linux.yml
@@ -5,7 +5,6 @@ channels:
   - defaults
 dependencies:
   - colour
-  - cython
   - dash
   - dask
   - dask-jobqueue

From b93aa70e72afd5701170f9a6f0ed36f6df94a3aa Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Wed, 30 Oct 2024 17:35:32 -0600
Subject: [PATCH 03/20] update requirements and env export, Mixture ->
 IdealMixture from thermosteam

---
 opgee-linux64.pkg_list.txt | 4 ++--
 opgee/thermodynamics.py    | 4 ++--
 requirements.txt           | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/opgee-linux64.pkg_list.txt b/opgee-linux64.pkg_list.txt
index cd1c29f9..b0c810af 100644
--- a/opgee-linux64.pkg_list.txt
+++ b/opgee-linux64.pkg_list.txt
@@ -49,7 +49,7 @@ cycler=0.12.1=pypi_0
 cython=3.0.11=py39h5eee18b_0
 cytoolz=0.12.2=py39h5eee18b_0
 dash=2.14.2=py39h06a4308_0
-dash-cytoscape=0.3.0=pypi_0
+dash-cytoscape=1.0.2=pypi_0
 dask=2024.5.0=py39h06a4308_0
 dask-core=2024.5.0=py39h06a4308_0
 dask-expr=1.1.0=py39h06a4308_0
@@ -238,7 +238,7 @@ tbb=2021.8.0=hdb19cb5_0
 tblib=1.7.0=pyhd3eb1b0_0
 tenacity=9.0.0=py39h06a4308_0
 thermo=0.2.25=pypi_0
-thermosteam=0.34.0=pypi_0
+thermosteam=0.45.0=pypi_0
 tk=8.6.14=h39e8969_0
 tomli=2.0.1=py39h06a4308_0
 toolz=0.12.0=py39h06a4308_0
diff --git a/opgee/thermodynamics.py b/opgee/thermodynamics.py
index 7f26aa02..0234764c 100644
--- a/opgee/thermodynamics.py
+++ b/opgee/thermodynamics.py
@@ -12,7 +12,7 @@
 import numpy as np
 import pint
 from pyXSteam.XSteam import XSteam
-from thermosteam import Chemical, Mixture
+from thermosteam import Chemical, IdealMixture
 
 from . import ureg
 from .core import OpgeeObject, STP, TemperaturePressure
@@ -239,7 +239,7 @@ def __init__(self, field, composition):
         self.field = field
         self.components = [name for name, fraction in self.composition]
         self.mol_fraction = mol_fraction = [fraction for name, fraction in self.composition]
-        self.mixture = mixture = Mixture.from_chemicals(self.components)
+        self.mixture = mixture = IdealMixture.from_chemicals(self.components)
         self.mol_weight = ureg.Quantity(mixture.MW(mol_fraction), "g/mol")
 
     def density(self):
diff --git a/requirements.txt b/requirements.txt
index d6d5697f..d14ebf6f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 # This file was generated by the script update-reqs.py. Manual edits may be lost.
 chemicals==1.1.4
 dash==2.14.2
-dash-cytoscape==0.3.0
+dash-cytoscape==1.0.2
 dask==2024.5.0
 dask-jobqueue==0.8.2
 fluids==1.0.24
@@ -24,4 +24,4 @@ sphinx==7.3.7
 sphinx-argparse==0.4.0
 sphinx_rtd_theme==2.0.0
 thermo==0.2.25
-thermosteam==0.34.0
+thermosteam==0.45.0

From e1b1242f4bfc2ba6d5e51318b5fab952ec97d2b2 Mon Sep 17 00:00:00 2001
From: Richard Plevin <rich@plevin.com>
Date: Thu, 31 Oct 2024 15:56:34 -0700
Subject: [PATCH 04/20] Update to python 3.11 and latest consistent set of
 packages

---
 Makefile            |  7 ++++++-
 py3-opgee-macos.yml |  9 +++++----
 requirements.txt    | 12 ++++++------
 update-reqs.py      | 17 ++++++++++++-----
 4 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/Makefile b/Makefile
index 8269a0d0..50f380fe 100644
--- a/Makefile
+++ b/Makefile
@@ -92,7 +92,12 @@ create-opgee: $(YML_FILE)
 install-opgee:
 	bash -l -c 'conda activate opgee && pip install -e .'
 
-rebuild-opgee: remove-opgee create-opgee install-opgee
+rebuild-opgee: remove-opgee create-opgee travis-reqs install-opgee
+
+# Generate a detailed package list to cache for validation of
+# environment on CI platform (currently github actions)
+linux-pkg-list:
+	conda list --export > opgee-linux64.pkg_list.txt
 
 NUITKA_EXE    = opgee.exe
 NUITKA_OUTDIR = /tmp/opgee-nuitka
diff --git a/py3-opgee-macos.yml b/py3-opgee-macos.yml
index 95692954..236f250b 100644
--- a/py3-opgee-macos.yml
+++ b/py3-opgee-macos.yml
@@ -20,7 +20,7 @@ dependencies:
   - pip
   - pydot
   - pytest
-  - python>=3.9.0,<3.10.0
+  - python>=3.11.0,<3.12.0
   - semver
   - setuptools
   - sphinx
@@ -32,6 +32,7 @@ dependencies:
     - dash-cytoscape
     - pyXSteam
     - thermosteam
-    - fluids==1.0.24
-    - chemicals==1.1.4
-    - thermo==0.2.25
+    - fluids
+    - chemicals
+    - thermo
+
diff --git a/requirements.txt b/requirements.txt
index d14ebf6f..89e0d702 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
 # This file was generated by the script update-reqs.py. Manual edits may be lost.
-chemicals==1.1.4
+chemicals==1.2.0
 dash==2.14.2
 dash-cytoscape==1.0.2
-dask==2024.5.0
+dask==2024.8.2
 dask-jobqueue==0.8.2
-fluids==1.0.24
+fluids==1.0.26
 future==0.18.3
 lxml==5.2.1
 matplotlib==3.9.2
@@ -17,11 +17,11 @@ pydot==1.4.2
 pytest==7.4.4
 python-dateutil==2.9.0post0
 pyxsteam==0.4.9
-scipy==1.13.1
+scipy==1.14.1
 semver==3.0.2
 setuptools==75.1.0
 sphinx==7.3.7
-sphinx-argparse==0.4.0
+sphinx-argparse==0.5.2
 sphinx_rtd_theme==2.0.0
-thermo==0.2.25
+thermo==0.3.0
 thermosteam==0.45.0
diff --git a/update-reqs.py b/update-reqs.py
index fbf6982f..61f60703 100755
--- a/update-reqs.py
+++ b/update-reqs.py
@@ -8,6 +8,8 @@
 
 REPO_DIR = os.path.dirname(__file__)
 
+Verbose = False
+
 def main():
     reqs_in  = os.path.join(REPO_DIR, "requirements.in")
     reqs_out = os.path.join(REPO_DIR, "requirements.txt")
@@ -16,13 +18,15 @@ def main():
         pkgs = [line.strip() for line in f.readlines() if not line.startswith('#')]
 
     expr = '(' + '|'.join(pkgs) + ')'
-    cmd = f"conda list -f '{expr}' | egrep -v '^#'"
-    # | egrep -i '{expr}'
+    cmd = f"conda list -n opgee | egrep -v '^#' | egrep '^{expr}\s+'"
+
+    if Verbose:
+        print(cmd)
 
-    # print(cmd)
     proc = subprocess.run(cmd, shell=True, capture_output=True, text=True)
 
-    # print(f"Lines:\n{proc.stdout}")
+    if Verbose:
+        print(f"Lines:\n{proc.stdout}")
 
     lines = proc.stdout.split('\n')
     with open(reqs_out, 'w') as f:
@@ -30,7 +34,10 @@ def main():
         for line in lines:
             if not line:
                 continue
-            # print(f"Line is '{line}'")
+
+            if Verbose:
+                print(f"Line is '{line}'")
+
             name, version, _, _ = re.split(r'\s+', line)
             f.write(f"{name}=={version}\n")
 

From 573666b48c3854526db72e84e52a06cbdeb97f4a Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 10:51:06 -0600
Subject: [PATCH 05/20] combine linux/mac into single config, update pkg list

---
 Makefile                                  |   4 +-
 opgee-linux64.pkg_list.txt                | 180 ++++++++++------------
 py3-opgee-linux.yml                       |  38 -----
 py3-opgee-macos.yml => py3-opgee-unix.yml |   6 +-
 4 files changed, 90 insertions(+), 138 deletions(-)
 delete mode 100644 py3-opgee-linux.yml
 rename py3-opgee-macos.yml => py3-opgee-unix.yml (100%)

diff --git a/Makefile b/Makefile
index 50f380fe..00262e0f 100644
--- a/Makefile
+++ b/Makefile
@@ -67,9 +67,9 @@ travis-reqs $(TRAVIS_REQS): requirements.in
 #
 UNAME=$(strip $(shell uname))
 ifeq ($(UNAME), Darwin)
-	YML_FILE=py3-opgee-macos.yml
+	YML_FILE=py3-opgee-unix.yml
 else ifeq ($(UNAME), Linux)
-	YML_FILE=py3-opgee-linux.yml
+	YML_FILE=py3-opgee-unix.yml
 else
 	YML_FILE=py3-opgee-win10.yml
 endif
diff --git a/opgee-linux64.pkg_list.txt b/opgee-linux64.pkg_list.txt
index b0c810af..575a1837 100644
--- a/opgee-linux64.pkg_list.txt
+++ b/opgee-linux64.pkg_list.txt
@@ -3,8 +3,8 @@
 # platform: linux-64
 _libgcc_mutex=0.1=main
 _openmp_mutex=5.1=1_gnu
-alabaster=0.7.16=py39h06a4308_0
-ansi2html=1.9.1=py39h06a4308_0
+alabaster=0.7.16=py311h06a4308_0
+ansi2html=1.9.1=py311h06a4308_0
 ansicolors=1.1.8=pypi_0
 appdirs=1.4.4=pyhd3eb1b0_0
 arrow-cpp=16.1.0=hc1eb8f0_0
@@ -23,50 +23,47 @@ aws-c-sdkutils=0.1.6=h5eee18b_0
 aws-checksums=0.1.13=h5eee18b_0
 aws-crt-cpp=0.18.16=h6a678d5_0
 aws-sdk-cpp=1.10.55=h721c034_0
-babel=2.11.0=py39h06a4308_0
+babel=2.11.0=py311h06a4308_0
 blas=1.0=openblas
-blinker=1.6.2=py39h06a4308_0
-bokeh=3.4.3=py39h2f386ee_0
+blinker=1.6.2=py311h06a4308_0
+bokeh=3.6.0=py311h06a4308_0
 boost-cpp=1.82.0=hdb19cb5_2
-bottleneck=1.3.7=py39ha9d4c09_0
-brotli-python=1.0.9=py39h6a678d5_8
+bottleneck=1.3.7=py311hf4808d0_0
+brotli-python=1.0.9=py311h6a678d5_8
 bzip2=1.0.8=h5eee18b_6
 c-ares=1.19.1=h5eee18b_0
 ca-certificates=2024.9.24=h06a4308_0
 cairo=1.16.0=hb05425b_5
-certifi=2024.8.30=py39h06a4308_0
-cffi=1.17.1=py39h1fdaa30_0
+certifi=2024.8.30=py311h06a4308_0
 charset-normalizer=3.3.2=pyhd3eb1b0_0
-chemicals=1.1.4=pypi_0
-click=8.1.7=py39h06a4308_0
-cloudpickle=3.0.0=py39h06a4308_0
+chemicals=1.2.0=pypi_0
+click=8.1.7=py311h06a4308_0
+cloudpickle=3.0.0=py311h06a4308_0
 colorama=0.4.6=pypi_0
 colorpalette=0.3.3=pypi_0
-colour=0.1.5=py39h06a4308_0
+colour=0.1.5=py311h06a4308_0
 commonmark=0.9.1=pyhd3eb1b0_0
-contourpy=1.2.0=py39hdb19cb5_0
+contourpy=1.2.0=py311hdb19cb5_0
 cycler=0.12.1=pypi_0
-cython=3.0.11=py39h5eee18b_0
-cytoolz=0.12.2=py39h5eee18b_0
-dash=2.14.2=py39h06a4308_0
+cytoolz=0.12.2=py311h5eee18b_0
+dash=2.14.2=py311h06a4308_0
 dash-cytoscape=1.0.2=pypi_0
-dask=2024.5.0=py39h06a4308_0
-dask-core=2024.5.0=py39h06a4308_0
-dask-expr=1.1.0=py39h06a4308_0
-dask-jobqueue=0.8.2=py39h06a4308_0
+dask=2024.8.2=py311h06a4308_0
+dask-core=2024.8.2=py311h06a4308_0
+dask-expr=1.1.13=py311h06a4308_0
+dask-jobqueue=0.8.2=py311h06a4308_0
 decorator=5.1.1=pypi_0
-distributed=2024.5.0=py39h06a4308_0
-docutils=0.18.1=py39h06a4308_3
+distributed=2024.8.2=py311h06a4308_0
+docutils=0.20.1=py311h38be061_3
 et-xmlfile=2.0.0=pypi_0
-exceptiongroup=1.2.0=py39h06a4308_0
 executing=2.1.0=pypi_0
 expat=2.6.3=h6a678d5_0
-flask=3.0.3=py39h06a4308_0
-flask-compress=1.13=py39h06a4308_0
+flask=3.0.3=py311h06a4308_0
+flask-compress=1.13=py311h06a4308_0
 flexcache=0.3=pyhd8ed1ab_0
 flexparser=0.3.1=pyhd8ed1ab_0
 flexsolve=0.5.7=pypi_0
-fluids=1.0.24=pypi_0
+fluids=1.0.26=pypi_0
 font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
 font-ttf-inconsolata=2.001=hcb22688_0
 font-ttf-source-code-pro=2.030=hd3eb1b0_0
@@ -78,15 +75,15 @@ fonttools=4.54.1=pypi_0
 free-properties=0.3.6=pypi_0
 freetype=2.12.1=h4a9f257_0
 fribidi=1.0.10=h7b6447c_0
-fsspec=2024.6.1=py39h06a4308_0
-future=0.18.3=py39h06a4308_0
+fsspec=2024.6.1=py311h06a4308_0
+future=0.18.3=py311h06a4308_0
 gdk-pixbuf=2.42.10=h5eee18b_1
 gflags=2.2.2=h6a678d5_1
 giflib=5.2.2=h5eee18b_0
 glib=2.78.4=h6a678d5_0
 glib-tools=2.78.4=h6a678d5_0
 glog=0.5.0=h6a678d5_1
-gobject-introspection=1.78.1=py39h42194e9_1
+gobject-introspection=1.78.1=py311h42194e9_1
 graphite2=1.3.14=h295c915_1
 graphviz=2.50.0=h1b29801_1
 gtk2=2.24.33=h73c1081_2
@@ -94,15 +91,14 @@ gts=0.7.6=hb67d8dd_3
 harfbuzz=4.3.0=hf52aaf7_2
 heapdict=1.0.1=pyhd3eb1b0_0
 icu=73.1=h6a678d5_0
-idna=3.7=py39h06a4308_0
-imagesize=1.4.1=py39h06a4308_0
-importlib-metadata=7.0.1=py39h06a4308_0
-importlib-resources=6.4.5=pypi_0
+idna=3.7=py311h06a4308_0
+imagesize=1.4.1=py311h06a4308_0
+importlib-metadata=7.0.1=py311h06a4308_0
 iniconfig=1.1.1=pyhd3eb1b0_0
-ipython=8.18.1=pypi_0
-itsdangerous=2.2.0=py39h06a4308_0
+ipython=8.29.0=pypi_0
+itsdangerous=2.2.0=py311h06a4308_0
 jedi=0.19.1=pypi_0
-jinja2=3.1.4=py39h06a4308_0
+jinja2=3.1.4=py311h06a4308_0
 jpeg=9e=h5eee18b_3
 kiwisolver=1.4.7=pypi_0
 krb5=1.20.1=h143b758_1
@@ -133,7 +129,6 @@ libnghttp2=1.57.0=h2d74bed_0
 libopenblas=0.3.21=h043d6bf_0
 libpng=1.6.39=h5eee18b_0
 libprotobuf=4.25.3=he621ea3_0
-libpython-static=3.9.20=h6a678d5_1
 librsvg=2.54.4=haac4a5d_4
 libssh2=1.11.0=h251f7ec_0
 libstdcxx-ng=11.2.0=h1234567_1
@@ -147,117 +142,112 @@ libxcb=1.15=h7f8727e_0
 libxml2=2.13.1=hfdd30dd_2
 libxslt=1.1.41=h097e994_0
 llvm-openmp=14.0.6=h9e868ea_0
-llvmlite=0.43.0=py39h6a678d5_0
-locket=1.0.0=py39h06a4308_0
-lxml=5.2.1=py39h57af460_1
-lz4=4.3.2=py39h5eee18b_0
+llvmlite=0.43.0=py311h6a678d5_0
+locket=1.0.0=py311h06a4308_0
+lxml=5.2.1=py311h57af460_1
+lz4=4.3.2=py311h5eee18b_0
 lz4-c=1.9.4=h6a678d5_1
-markupsafe=2.1.3=py39h5eee18b_0
+markupsafe=2.1.3=py311h5eee18b_0
 matplotlib=3.9.2=pypi_0
 matplotlib-inline=0.1.7=pypi_0
-msgpack-python=1.0.3=py39hd09550d_0
+msgpack-python=1.0.3=py311hdb19cb5_0
 ncurses=6.4=h6a678d5_0
-nest-asyncio=1.6.0=py39h06a4308_0
-networkx=3.2.1=py39h06a4308_0
+nest-asyncio=1.6.0=py311h06a4308_0
+networkx=3.2.1=py311h06a4308_0
 ninja=1.10.2=h06a4308_5
 ninja-base=1.10.2=hd09550d_5
 nspr=4.35=h6a678d5_0
 nss=3.89.1=h6a678d5_0
-nuitka=1.5.8=py39h5eee18b_0
-numba=0.60.0=py39h6a678d5_0
-numexpr=2.10.1=py39hd28fd6d_0
-numpy=1.26.4=py39heeff2f4_0
-numpy-base=1.26.4=py39h8a23956_0
+numba=0.60.0=py311ha02d727_0
+numexpr=2.10.1=py311hd28fd6d_0
+numpy=1.26.4=py311h24aa872_0
+numpy-base=1.26.4=py311hbfb1bba_0
 openjpeg=2.5.2=he7f1fd0_0
 openpyxl=3.1.5=pypi_0
 openssl=3.0.15=h5eee18b_0
 opgee=4.0a0=dev_0
 orc=2.0.1=h2d29ad5_0
-ordered-set=4.1.0=py39h06a4308_0
-packaging=24.1=py39h06a4308_0
-pandas=2.2.2=py39h6a678d5_0
+packaging=24.1=py311h06a4308_0
+pandas=2.2.2=py311ha02d727_0
 pango=1.50.7=h05da053_0
 parso=0.8.4=pypi_0
-partd=1.4.1=py39h06a4308_0
+partd=1.4.1=py311h06a4308_0
 pcre2=10.42=hebb0a14_1
 pexpect=4.9.0=pypi_0
-pillow=9.4.0=py39h6a678d5_0
+pillow=9.4.0=py311h6a678d5_0
 pint=0.24.3=pyhd8ed1ab_0
 pint-pandas=0.6.2=pyhd8ed1ab_0
-pip=24.2=py39h06a4308_0
+pip=24.2=py311h06a4308_0
 pixman=0.40.0=h7f8727e_1
-plotly=5.24.1=py39h2f386ee_0
-pluggy=1.0.0=py39h06a4308_1
+plotly=5.24.1=py311h92b7b1e_0
+pluggy=1.0.0=py311h06a4308_1
 poppler=24.09.0=h55ad6a6_0
 poppler-data=0.4.11=h06a4308_1
 prompt-toolkit=3.0.48=pypi_0
-psutil=5.9.0=py39h5eee18b_0
+psutil=5.9.0=py311h5eee18b_0
 ptyprocess=0.7.0=pypi_0
 pure-eval=0.2.3=pypi_0
-pyarrow=16.1.0=py39h1128e8f_0
-pycparser=2.21=pyhd3eb1b0_0
-pydot=1.4.2=py39h06a4308_0
+pyarrow=16.1.0=py311ha02d727_0
+pydot=1.4.2=py311h06a4308_0
 pyglet=2.0.18=pypi_0
-pygments=2.15.1=py39h06a4308_1
+pygments=2.15.1=py311h06a4308_1
 pyparsing=2.4.7=pyhd3eb1b0_0
-pysocks=1.7.1=py39h06a4308_0
-pytest=7.4.4=py39h06a4308_0
-python=3.9.20=he870216_1
-python-dateutil=2.9.0post0=py39h06a4308_2
-python-graphviz=0.20.1=py39h06a4308_0
-python-lmdb=1.4.1=py39h6a678d5_0
+pysocks=1.7.1=py311h06a4308_0
+pytest=7.4.4=py311h06a4308_0
+python=3.11.10=he870216_0
+python-dateutil=2.9.0post0=py311h06a4308_2
+python-lmdb=1.4.1=py311h6a678d5_0
 python-tzdata=2023.3=pyhd3eb1b0_0
-pytz=2024.1=py39h06a4308_0
+python_abi=3.11=2_cp311
+pytz=2024.1=py311h06a4308_0
 pyxsteam=0.4.9=pypi_0
-pyyaml=6.0.2=py39h5eee18b_0
+pyyaml=6.0.2=py311h5eee18b_0
 re2=2022.04.01=h295c915_0
 readline=8.2=h5eee18b_0
-requests=2.32.3=py39h06a4308_0
+requests=2.32.3=py311h06a4308_0
 retrying=1.3.3=pyhd3eb1b0_2
 s2n=1.3.27=hdbd6064_0
-scipy=1.13.1=pypi_0
-semver=3.0.2=py39h06a4308_0
-setuptools=75.1.0=py39h06a4308_0
+scipy=1.14.1=pypi_0
+semver=3.0.2=py311h06a4308_0
+setuptools=75.1.0=py311h06a4308_0
 six=1.16.0=pyhd3eb1b0_1
 snappy=1.2.1=h6a678d5_0
 snowballstemmer=2.2.0=pyhd3eb1b0_0
 sortedcontainers=2.4.0=pyhd3eb1b0_0
-sphinx=7.3.7=py39h5eee18b_0
-sphinx-argparse=0.4.0=pyhd8ed1ab_0
-sphinx_rtd_theme=2.0.0=py39h06a4308_0
+sphinx=7.3.7=py311h5eee18b_0
+sphinx-argparse=0.5.2=pyhd8ed1ab_0
+sphinx_rtd_theme=2.0.0=py311h06a4308_0
 sphinxcontrib-applehelp=1.0.2=pyhd3eb1b0_0
 sphinxcontrib-devhelp=1.0.2=pyhd3eb1b0_0
 sphinxcontrib-htmlhelp=2.0.0=pyhd3eb1b0_0
-sphinxcontrib-jquery=4.1=py39h06a4308_0
+sphinxcontrib-jquery=4.1=py311h06a4308_0
 sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
 sphinxcontrib-qthelp=1.0.3=pyhd3eb1b0_0
-sphinxcontrib-serializinghtml=1.1.10=py39h06a4308_0
+sphinxcontrib-serializinghtml=1.1.10=py311h06a4308_0
 sqlite=3.45.3=h5eee18b_0
 stack-data=0.6.3=pypi_0
 tbb=2021.8.0=hdb19cb5_0
 tblib=1.7.0=pyhd3eb1b0_0
-tenacity=9.0.0=py39h06a4308_0
-thermo=0.2.25=pypi_0
+tenacity=9.0.0=py311h06a4308_0
+thermo=0.3.0=pypi_0
 thermosteam=0.45.0=pypi_0
 tk=8.6.14=h39e8969_0
-tomli=2.0.1=py39h06a4308_0
-toolz=0.12.0=py39h06a4308_0
-tornado=6.4.1=py39h5eee18b_0
+toolz=0.12.0=py311h06a4308_0
+tornado=6.4.1=py311h5eee18b_0
 traitlets=5.14.3=pypi_0
-typing-extensions=4.11.0=py39h06a4308_0
-typing_extensions=4.11.0=py39h06a4308_0
+typing-extensions=4.11.0=py311h06a4308_0
+typing_extensions=4.11.0=py311h06a4308_0
 tzdata=2024b=h04d1e81_0
-urllib3=2.2.3=py39h06a4308_0
+urllib3=2.2.3=py311h06a4308_0
 utf8proc=2.6.1=h5eee18b_1
 wcwidth=0.2.13=pypi_0
-werkzeug=3.0.3=py39h06a4308_0
-wheel=0.44.0=py39h06a4308_0
+werkzeug=3.0.3=py311h06a4308_0
+wheel=0.44.0=py311h06a4308_0
 xlrd=2.0.1=pypi_0
-xyzservices=2022.9.0=py39h06a4308_1
+xyzservices=2022.9.0=py311h06a4308_1
 xz=5.4.6=h5eee18b_1
 yaml=0.2.5=h7b6447c_0
-zict=3.0.0=py39h06a4308_0
-zipp=3.20.2=py39h06a4308_0
+zict=3.0.0=py311h06a4308_0
+zipp=3.20.2=py311h06a4308_0
 zlib=1.2.13=h5eee18b_1
-zstandard=0.23.0=py39h2c38b39_0
 zstd=1.5.6=hc292b87_0
diff --git a/py3-opgee-linux.yml b/py3-opgee-linux.yml
deleted file mode 100644
index e22cdae1..00000000
--- a/py3-opgee-linux.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-name: opgee
-channels:
-  - anaconda
-  - conda-forge
-  - defaults
-dependencies:
-  - colour
-  - dash
-  - dask
-  - dask-jobqueue
-  - graphviz
-  - jinja2
-  - llvm-openmp
-  - lxml
-  - networkx
-  - numba
-  - numpy
-  - pandas
-  - pint
-  - pint-pandas
-  - pip
-  - pydot
-  - pytest
-  - python-graphviz
-  - python>=3.9.0,<3.10.0
-  - semver
-  - setuptools
-  - sphinx
-  - sphinx-argparse
-  - sphinx_rtd_theme
-  - sphinxcontrib-serializinghtml
-  - pip:
-    - dash-cytoscape
-    - pyXSteam
-    - thermosteam
-    - fluids==1.0.24
-    - chemicals==1.1.4
-    - thermo==0.2.25
diff --git a/py3-opgee-macos.yml b/py3-opgee-unix.yml
similarity index 100%
rename from py3-opgee-macos.yml
rename to py3-opgee-unix.yml
index 236f250b..0fd0578d 100644
--- a/py3-opgee-macos.yml
+++ b/py3-opgee-unix.yml
@@ -29,10 +29,10 @@ dependencies:
   - sphinxcontrib-serializinghtml
   - pip:
     # - nuitka            # experimental; moved here because conda version is very outdated
+    - chemicals
     - dash-cytoscape
-    - pyXSteam
-    - thermosteam
     - fluids
-    - chemicals
+    - pyXSteam
     - thermo
+    - thermosteam
 

From 3103a453e81ab8bd9500ebf1bb64379f4d19294a Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 21:38:37 -0600
Subject: [PATCH 06/20] add matrix to runner, all conda envs are equivalent,
 tweak names, update reqs

---
 .github/workflows/opgee-test.yml |  19 +-
 Makefile                         |   4 +-
 opgee-linux64.pkg_list.txt       | 253 ---------------------------
 opgee.pkg_list.txt               | 289 +++++++++++++++++++++++++++++++
 py3-opgee-unix.yml               |  13 +-
 py3-opgee-win10.yml              |   1 -
 requirements.txt                 |  31 ++--
 update-reqs.py                   |   2 +-
 8 files changed, 325 insertions(+), 287 deletions(-)
 delete mode 100644 opgee-linux64.pkg_list.txt
 create mode 100644 opgee.pkg_list.txt

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index 933202ee..67107c6e 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -7,18 +7,26 @@ on:
       - dev
 
 jobs:
-  test-linux:
-    runs-on: ubuntu-latest
+  test:
     strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        arch: [x64, arm64]
+        exclude:
+          - os: ubuntu-latest
+            arch: arm64
+          - os: macos-latest
+            arch: x64
       max-parallel: 5
+    runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -el {0}
     env:
       OPGEE_HOME: ${{ github.workspace }}/tests/files
       CI: 'true'
-      opgee_pkg_list: 'opgee-linux64.pkg_list.txt'
-      opgee_linux_yml: 'py3-opgee-linux.yml'
+      opgee_pkg_list: 'opgee.pkg_list.txt'
+      opgee_env_yml: 'py3-opgee-unix.yml'
     steps:
     - uses: actions/checkout@v4
     - name: Cache pip dependencies
@@ -48,9 +56,8 @@ jobs:
           ${{ runner.os }}-conda-${{ runner.arch }}-${{ hashFiles(env.opgee_pkg_list) }}-${{ env.CACHE_NUMBER }}
     - name: Update Conda env and pip dependencies
       run: |
-        conda env update -n opgee -f $opgee_linux_yml
+        conda env update -n opgee -f $opgee_env_yml
         pip install -e .
-        python -m pip install -e .
         pip install pytest-cov codecov coveralls PyYAML
       if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.cache-hit != 'true'
     - name: Run unit tests with coverage
diff --git a/Makefile b/Makefile
index 00262e0f..e5658ec1 100644
--- a/Makefile
+++ b/Makefile
@@ -96,8 +96,8 @@ rebuild-opgee: remove-opgee create-opgee travis-reqs install-opgee
 
 # Generate a detailed package list to cache for validation of
 # environment on CI platform (currently github actions)
-linux-pkg-list:
-	conda list --export > opgee-linux64.pkg_list.txt
+env-pkg-list:
+	conda list --export > opgee.pkg_list.txt
 
 NUITKA_EXE    = opgee.exe
 NUITKA_OUTDIR = /tmp/opgee-nuitka
diff --git a/opgee-linux64.pkg_list.txt b/opgee-linux64.pkg_list.txt
deleted file mode 100644
index 575a1837..00000000
--- a/opgee-linux64.pkg_list.txt
+++ /dev/null
@@ -1,253 +0,0 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-64
-_libgcc_mutex=0.1=main
-_openmp_mutex=5.1=1_gnu
-alabaster=0.7.16=py311h06a4308_0
-ansi2html=1.9.1=py311h06a4308_0
-ansicolors=1.1.8=pypi_0
-appdirs=1.4.4=pyhd3eb1b0_0
-arrow-cpp=16.1.0=hc1eb8f0_0
-asttokens=2.4.1=pypi_0
-atk-1.0=2.36.0=ha1a6a79_0
-aws-c-auth=0.6.19=h5eee18b_0
-aws-c-cal=0.5.20=hdbd6064_0
-aws-c-common=0.8.5=h5eee18b_0
-aws-c-compression=0.2.16=h5eee18b_0
-aws-c-event-stream=0.2.15=h6a678d5_0
-aws-c-http=0.6.25=h5eee18b_0
-aws-c-io=0.13.10=h5eee18b_0
-aws-c-mqtt=0.7.13=h5eee18b_0
-aws-c-s3=0.1.51=hdbd6064_0
-aws-c-sdkutils=0.1.6=h5eee18b_0
-aws-checksums=0.1.13=h5eee18b_0
-aws-crt-cpp=0.18.16=h6a678d5_0
-aws-sdk-cpp=1.10.55=h721c034_0
-babel=2.11.0=py311h06a4308_0
-blas=1.0=openblas
-blinker=1.6.2=py311h06a4308_0
-bokeh=3.6.0=py311h06a4308_0
-boost-cpp=1.82.0=hdb19cb5_2
-bottleneck=1.3.7=py311hf4808d0_0
-brotli-python=1.0.9=py311h6a678d5_8
-bzip2=1.0.8=h5eee18b_6
-c-ares=1.19.1=h5eee18b_0
-ca-certificates=2024.9.24=h06a4308_0
-cairo=1.16.0=hb05425b_5
-certifi=2024.8.30=py311h06a4308_0
-charset-normalizer=3.3.2=pyhd3eb1b0_0
-chemicals=1.2.0=pypi_0
-click=8.1.7=py311h06a4308_0
-cloudpickle=3.0.0=py311h06a4308_0
-colorama=0.4.6=pypi_0
-colorpalette=0.3.3=pypi_0
-colour=0.1.5=py311h06a4308_0
-commonmark=0.9.1=pyhd3eb1b0_0
-contourpy=1.2.0=py311hdb19cb5_0
-cycler=0.12.1=pypi_0
-cytoolz=0.12.2=py311h5eee18b_0
-dash=2.14.2=py311h06a4308_0
-dash-cytoscape=1.0.2=pypi_0
-dask=2024.8.2=py311h06a4308_0
-dask-core=2024.8.2=py311h06a4308_0
-dask-expr=1.1.13=py311h06a4308_0
-dask-jobqueue=0.8.2=py311h06a4308_0
-decorator=5.1.1=pypi_0
-distributed=2024.8.2=py311h06a4308_0
-docutils=0.20.1=py311h38be061_3
-et-xmlfile=2.0.0=pypi_0
-executing=2.1.0=pypi_0
-expat=2.6.3=h6a678d5_0
-flask=3.0.3=py311h06a4308_0
-flask-compress=1.13=py311h06a4308_0
-flexcache=0.3=pyhd8ed1ab_0
-flexparser=0.3.1=pyhd8ed1ab_0
-flexsolve=0.5.7=pypi_0
-fluids=1.0.26=pypi_0
-font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
-font-ttf-inconsolata=2.001=hcb22688_0
-font-ttf-source-code-pro=2.030=hd3eb1b0_0
-font-ttf-ubuntu=0.83=h8b1ccd4_0
-fontconfig=2.14.1=h55d465d_3
-fonts-anaconda=1=h8fa9717_0
-fonts-conda-ecosystem=1=hd3eb1b0_0
-fonttools=4.54.1=pypi_0
-free-properties=0.3.6=pypi_0
-freetype=2.12.1=h4a9f257_0
-fribidi=1.0.10=h7b6447c_0
-fsspec=2024.6.1=py311h06a4308_0
-future=0.18.3=py311h06a4308_0
-gdk-pixbuf=2.42.10=h5eee18b_1
-gflags=2.2.2=h6a678d5_1
-giflib=5.2.2=h5eee18b_0
-glib=2.78.4=h6a678d5_0
-glib-tools=2.78.4=h6a678d5_0
-glog=0.5.0=h6a678d5_1
-gobject-introspection=1.78.1=py311h42194e9_1
-graphite2=1.3.14=h295c915_1
-graphviz=2.50.0=h1b29801_1
-gtk2=2.24.33=h73c1081_2
-gts=0.7.6=hb67d8dd_3
-harfbuzz=4.3.0=hf52aaf7_2
-heapdict=1.0.1=pyhd3eb1b0_0
-icu=73.1=h6a678d5_0
-idna=3.7=py311h06a4308_0
-imagesize=1.4.1=py311h06a4308_0
-importlib-metadata=7.0.1=py311h06a4308_0
-iniconfig=1.1.1=pyhd3eb1b0_0
-ipython=8.29.0=pypi_0
-itsdangerous=2.2.0=py311h06a4308_0
-jedi=0.19.1=pypi_0
-jinja2=3.1.4=py311h06a4308_0
-jpeg=9e=h5eee18b_3
-kiwisolver=1.4.7=pypi_0
-krb5=1.20.1=h143b758_1
-lcms2=2.12=h3be6417_0
-ld_impl_linux-64=2.40=h12ee557_0
-lerc=3.0=h295c915_0
-libabseil=20240116.2=cxx17_h6a678d5_0
-libboost=1.82.0=h109eef0_2
-libbrotlicommon=1.0.9=h5eee18b_8
-libbrotlidec=1.0.9=h5eee18b_8
-libbrotlienc=1.0.9=h5eee18b_8
-libcurl=8.9.1=h251f7ec_0
-libdeflate=1.17=h5eee18b_1
-libedit=3.1.20230828=h5eee18b_0
-libev=4.33=h7f8727e_1
-libevent=2.1.12=hdbd6064_1
-libffi=3.4.4=h6a678d5_1
-libgcc-ng=11.2.0=h1234567_1
-libgd=2.3.3=h6a678d5_3
-libgfortran-ng=11.2.0=h00389a5_1
-libgfortran5=11.2.0=h1234567_1
-libglib=2.78.4=hdc74915_0
-libgomp=11.2.0=h1234567_1
-libgrpc=1.62.2=h2d74bed_0
-libiconv=1.16=h5eee18b_3
-libllvm14=14.0.6=hecde1de_4
-libnghttp2=1.57.0=h2d74bed_0
-libopenblas=0.3.21=h043d6bf_0
-libpng=1.6.39=h5eee18b_0
-libprotobuf=4.25.3=he621ea3_0
-librsvg=2.54.4=haac4a5d_4
-libssh2=1.11.0=h251f7ec_0
-libstdcxx-ng=11.2.0=h1234567_1
-libthrift=0.15.0=h1795dd8_2
-libtiff=4.5.1=h6a678d5_0
-libtool=2.4.6=h6a678d5_1009
-libuuid=1.41.5=h5eee18b_0
-libwebp=1.2.4=h11a3e52_1
-libwebp-base=1.2.4=h5eee18b_1
-libxcb=1.15=h7f8727e_0
-libxml2=2.13.1=hfdd30dd_2
-libxslt=1.1.41=h097e994_0
-llvm-openmp=14.0.6=h9e868ea_0
-llvmlite=0.43.0=py311h6a678d5_0
-locket=1.0.0=py311h06a4308_0
-lxml=5.2.1=py311h57af460_1
-lz4=4.3.2=py311h5eee18b_0
-lz4-c=1.9.4=h6a678d5_1
-markupsafe=2.1.3=py311h5eee18b_0
-matplotlib=3.9.2=pypi_0
-matplotlib-inline=0.1.7=pypi_0
-msgpack-python=1.0.3=py311hdb19cb5_0
-ncurses=6.4=h6a678d5_0
-nest-asyncio=1.6.0=py311h06a4308_0
-networkx=3.2.1=py311h06a4308_0
-ninja=1.10.2=h06a4308_5
-ninja-base=1.10.2=hd09550d_5
-nspr=4.35=h6a678d5_0
-nss=3.89.1=h6a678d5_0
-numba=0.60.0=py311ha02d727_0
-numexpr=2.10.1=py311hd28fd6d_0
-numpy=1.26.4=py311h24aa872_0
-numpy-base=1.26.4=py311hbfb1bba_0
-openjpeg=2.5.2=he7f1fd0_0
-openpyxl=3.1.5=pypi_0
-openssl=3.0.15=h5eee18b_0
-opgee=4.0a0=dev_0
-orc=2.0.1=h2d29ad5_0
-packaging=24.1=py311h06a4308_0
-pandas=2.2.2=py311ha02d727_0
-pango=1.50.7=h05da053_0
-parso=0.8.4=pypi_0
-partd=1.4.1=py311h06a4308_0
-pcre2=10.42=hebb0a14_1
-pexpect=4.9.0=pypi_0
-pillow=9.4.0=py311h6a678d5_0
-pint=0.24.3=pyhd8ed1ab_0
-pint-pandas=0.6.2=pyhd8ed1ab_0
-pip=24.2=py311h06a4308_0
-pixman=0.40.0=h7f8727e_1
-plotly=5.24.1=py311h92b7b1e_0
-pluggy=1.0.0=py311h06a4308_1
-poppler=24.09.0=h55ad6a6_0
-poppler-data=0.4.11=h06a4308_1
-prompt-toolkit=3.0.48=pypi_0
-psutil=5.9.0=py311h5eee18b_0
-ptyprocess=0.7.0=pypi_0
-pure-eval=0.2.3=pypi_0
-pyarrow=16.1.0=py311ha02d727_0
-pydot=1.4.2=py311h06a4308_0
-pyglet=2.0.18=pypi_0
-pygments=2.15.1=py311h06a4308_1
-pyparsing=2.4.7=pyhd3eb1b0_0
-pysocks=1.7.1=py311h06a4308_0
-pytest=7.4.4=py311h06a4308_0
-python=3.11.10=he870216_0
-python-dateutil=2.9.0post0=py311h06a4308_2
-python-lmdb=1.4.1=py311h6a678d5_0
-python-tzdata=2023.3=pyhd3eb1b0_0
-python_abi=3.11=2_cp311
-pytz=2024.1=py311h06a4308_0
-pyxsteam=0.4.9=pypi_0
-pyyaml=6.0.2=py311h5eee18b_0
-re2=2022.04.01=h295c915_0
-readline=8.2=h5eee18b_0
-requests=2.32.3=py311h06a4308_0
-retrying=1.3.3=pyhd3eb1b0_2
-s2n=1.3.27=hdbd6064_0
-scipy=1.14.1=pypi_0
-semver=3.0.2=py311h06a4308_0
-setuptools=75.1.0=py311h06a4308_0
-six=1.16.0=pyhd3eb1b0_1
-snappy=1.2.1=h6a678d5_0
-snowballstemmer=2.2.0=pyhd3eb1b0_0
-sortedcontainers=2.4.0=pyhd3eb1b0_0
-sphinx=7.3.7=py311h5eee18b_0
-sphinx-argparse=0.5.2=pyhd8ed1ab_0
-sphinx_rtd_theme=2.0.0=py311h06a4308_0
-sphinxcontrib-applehelp=1.0.2=pyhd3eb1b0_0
-sphinxcontrib-devhelp=1.0.2=pyhd3eb1b0_0
-sphinxcontrib-htmlhelp=2.0.0=pyhd3eb1b0_0
-sphinxcontrib-jquery=4.1=py311h06a4308_0
-sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
-sphinxcontrib-qthelp=1.0.3=pyhd3eb1b0_0
-sphinxcontrib-serializinghtml=1.1.10=py311h06a4308_0
-sqlite=3.45.3=h5eee18b_0
-stack-data=0.6.3=pypi_0
-tbb=2021.8.0=hdb19cb5_0
-tblib=1.7.0=pyhd3eb1b0_0
-tenacity=9.0.0=py311h06a4308_0
-thermo=0.3.0=pypi_0
-thermosteam=0.45.0=pypi_0
-tk=8.6.14=h39e8969_0
-toolz=0.12.0=py311h06a4308_0
-tornado=6.4.1=py311h5eee18b_0
-traitlets=5.14.3=pypi_0
-typing-extensions=4.11.0=py311h06a4308_0
-typing_extensions=4.11.0=py311h06a4308_0
-tzdata=2024b=h04d1e81_0
-urllib3=2.2.3=py311h06a4308_0
-utf8proc=2.6.1=h5eee18b_1
-wcwidth=0.2.13=pypi_0
-werkzeug=3.0.3=py311h06a4308_0
-wheel=0.44.0=py311h06a4308_0
-xlrd=2.0.1=pypi_0
-xyzservices=2022.9.0=py311h06a4308_1
-xz=5.4.6=h5eee18b_1
-yaml=0.2.5=h7b6447c_0
-zict=3.0.0=py311h06a4308_0
-zipp=3.20.2=py311h06a4308_0
-zlib=1.2.13=h5eee18b_1
-zstd=1.5.6=hc292b87_0
diff --git a/opgee.pkg_list.txt b/opgee.pkg_list.txt
new file mode 100644
index 00000000..fca28feb
--- /dev/null
+++ b/opgee.pkg_list.txt
@@ -0,0 +1,289 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+_libgcc_mutex=0.1=conda_forge
+_openmp_mutex=4.5=2_gnu
+alabaster=1.0.0=pyhd8ed1ab_0
+ansicolors=1.1.8=pypi_0
+appdirs=1.4.4=pyh9f0ad1d_0
+asttokens=2.4.1=pypi_0
+atk-1.0=2.38.0=h04ea711_2
+aws-c-auth=0.7.31=hcdce11a_5
+aws-c-cal=0.7.4=hd3f4568_4
+aws-c-common=0.9.31=hb9d3cd8_0
+aws-c-compression=0.2.19=hf20e7d7_4
+aws-c-event-stream=0.5.0=h72d8268_0
+aws-c-http=0.8.10=h6bb76cc_5
+aws-c-io=0.14.20=h389d861_2
+aws-c-mqtt=0.10.7=had056f2_5
+aws-c-s3=0.7.0=hc85afc5_0
+aws-c-sdkutils=0.1.19=hf20e7d7_6
+aws-checksums=0.1.20=hf20e7d7_3
+aws-crt-cpp=0.29.0=h07ed512_0
+aws-sdk-cpp=1.11.407=h9c41b47_6
+azure-core-cpp=1.14.0=h5cfcd09_0
+azure-identity-cpp=1.10.0=h113e628_0
+azure-storage-blobs-cpp=12.13.0=h3cf044e_1
+azure-storage-common-cpp=12.8.0=h736e048_1
+azure-storage-files-datalake-cpp=12.12.0=ha633028_1
+babel=2.14.0=pyhd8ed1ab_0
+blinker=1.8.2=pyhd8ed1ab_0
+bokeh=3.6.0=pyhd8ed1ab_0
+brotli=1.1.0=hb9d3cd8_2
+brotli-bin=1.1.0=hb9d3cd8_2
+brotli-python=1.1.0=py311hfdbb021_2
+bzip2=1.0.8=h4bc722e_7
+c-ares=1.34.2=heb4867d_0
+ca-certificates=2024.8.30=hbcca054_0
+cairo=1.18.0=hebfffa5_3
+certifi=2024.8.30=pyhd8ed1ab_0
+cffi=1.17.1=py311hf29c0ef_0
+charset-normalizer=3.4.0=pyhd8ed1ab_0
+chemicals=1.2.0=pyhd8ed1ab_0
+click=8.1.7=unix_pyh707e725_0
+cloudpickle=3.1.0=pyhd8ed1ab_1
+colorama=0.4.6=pyhd8ed1ab_0
+colorpalette=0.3.3=pypi_0
+commonmark=0.9.1=py_0
+contourpy=1.3.0=py311hd18a35c_2
+coolprop=6.6.0=py311hfdbb021_3
+cpython=3.11.10=py311hd8ed1ab_3
+cycler=0.12.1=pyhd8ed1ab_0
+cytoolz=1.0.0=py311h9ecbd09_1
+dash=2.18.1=pyhd8ed1ab_0
+dash-core-components=2.0.0=pypi_0
+dash-cytoscape=1.0.2=pypi_0
+dash-html-components=2.0.0=pypi_0
+dash-table=5.0.0=pypi_0
+dask=2024.10.0=pyhd8ed1ab_0
+dask-core=2024.10.0=pyhd8ed1ab_0
+dask-expr=1.1.16=pyhd8ed1ab_0
+dask-jobqueue=0.9.0=pyhd8ed1ab_0
+decorator=5.1.1=pypi_0
+distributed=2024.10.0=pyhd8ed1ab_0
+docutils=0.21.2=pyhd8ed1ab_0
+et-xmlfile=2.0.0=pypi_0
+exceptiongroup=1.2.2=pyhd8ed1ab_0
+executing=2.1.0=pypi_0
+flask=3.0.3=pyhd8ed1ab_0
+flexcache=0.3=pyhd8ed1ab_0
+flexparser=0.3.1=pyhd8ed1ab_0
+flexsolve=0.5.7=pypi_0
+fluids=1.0.26=pyhff2d567_0
+font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+font-ttf-inconsolata=3.000=h77eed37_0
+font-ttf-source-code-pro=2.038=h77eed37_0
+font-ttf-ubuntu=0.83=h77eed37_3
+fontconfig=2.15.0=h7e30c49_1
+fonts-conda-ecosystem=1=0
+fonts-conda-forge=1=0
+fonttools=4.54.1=py311h2dc5d0c_1
+free-properties=0.3.6=pypi_0
+freetype=2.12.1=h267a509_2
+fribidi=1.0.10=h36c2ea0_0
+fsspec=2024.10.0=pyhff2d567_0
+future=1.0.0=pyhd8ed1ab_0
+fuzzywuzzy=0.18.0=pyhd8ed1ab_0
+gdk-pixbuf=2.42.12=hb9ae30d_0
+gflags=2.2.2=h5888daf_1005
+glog=0.7.1=hbabe93e_0
+gmp=6.3.0=hac33072_2
+gmpy2=2.1.5=py311h0f6cedb_2
+graphite2=1.3.13=h59595ed_1003
+graphviz=12.0.0=hba01fac_0
+gtk2=2.24.33=h6470451_5
+gts=0.7.6=h977cf35_4
+h2=4.1.0=pyhd8ed1ab_0
+harfbuzz=9.0.0=hda332d3_1
+hpack=4.0.0=pyh9f0ad1d_0
+hyperframe=6.0.1=pyhd8ed1ab_0
+icu=75.1=he02047a_0
+idna=3.10=pyhd8ed1ab_0
+imagesize=1.4.1=pyhd8ed1ab_0
+importlib-metadata=8.5.0=pyha770c72_0
+importlib_metadata=8.5.0=hd8ed1ab_0
+iniconfig=2.0.0=pyhd8ed1ab_0
+ipython=8.29.0=pypi_0
+itsdangerous=2.2.0=pyhd8ed1ab_0
+jedi=0.19.1=pypi_0
+jinja2=3.1.4=pyhd8ed1ab_0
+keyutils=1.6.1=h166bdaf_0
+kiwisolver=1.4.7=py311hd18a35c_0
+krb5=1.21.3=h659f571_0
+lcms2=2.16=hb7c19ff_0
+ld_impl_linux-64=2.43=h712a8e2_2
+lerc=4.0.0=h27087fc_0
+levenshtein=0.26.1=py311hfdbb021_0
+libabseil=20240722.0=cxx17_h5888daf_1
+libarrow=18.0.0=ha5db6c2_0_cpu
+libarrow-acero=18.0.0=h5888daf_0_cpu
+libarrow-dataset=18.0.0=h5888daf_0_cpu
+libarrow-substrait=18.0.0=he882d9a_0_cpu
+libblas=3.9.0=25_linux64_openblas
+libbrotlicommon=1.1.0=hb9d3cd8_2
+libbrotlidec=1.1.0=hb9d3cd8_2
+libbrotlienc=1.1.0=hb9d3cd8_2
+libcblas=3.9.0=25_linux64_openblas
+libcrc32c=1.1.2=h9c3ff4c_0
+libcurl=8.10.1=hbbe4b11_0
+libdeflate=1.22=hb9d3cd8_0
+libedit=3.1.20191231=he28a2e2_2
+libev=4.33=hd590300_2
+libevent=2.1.12=hf998b51_1
+libexpat=2.6.3=h5888daf_0
+libffi=3.4.2=h7f98852_5
+libgcc=14.2.0=h77fa898_1
+libgcc-ng=14.2.0=h69a702a_1
+libgd=2.3.3=hd3e95f3_10
+libgfortran=14.2.0=h69a702a_1
+libgfortran-ng=14.2.0=h69a702a_1
+libgfortran5=14.2.0=hd5240d6_1
+libglib=2.82.2=h2ff4ddf_0
+libgomp=14.2.0=h77fa898_1
+libgoogle-cloud=2.30.0=h438788a_0
+libgoogle-cloud-storage=2.30.0=h0121fbd_0
+libgrpc=1.65.5=hf5c653b_0
+libiconv=1.17=hd590300_2
+libjpeg-turbo=3.0.0=hd590300_1
+liblapack=3.9.0=25_linux64_openblas
+libllvm14=14.0.6=hcd5def8_4
+libnghttp2=1.64.0=h161d5f1_0
+libnsl=2.0.1=hd590300_0
+libopenblas=0.3.28=pthreads_h94d23a6_0
+libparquet=18.0.0=h6bd9018_0_cpu
+libpng=1.6.44=hadc24fc_0
+libprotobuf=5.27.5=h5b01275_2
+libre2-11=2024.07.02=hbbce691_1
+librsvg=2.58.4=hc0ffecb_0
+libsqlite=3.47.0=hadc24fc_1
+libssh2=1.11.0=h0841786_0
+libstdcxx=14.2.0=hc0a3c3a_1
+libstdcxx-ng=14.2.0=h4852527_1
+libthrift=0.21.0=h0e7cc3e_0
+libtiff=4.7.0=he137b08_1
+libutf8proc=2.8.0=h166bdaf_0
+libuuid=2.38.1=h0b41bf4_0
+libwebp-base=1.4.0=hd590300_0
+libxcb=1.17.0=h8a09558_0
+libxcrypt=4.4.36=hd590300_1
+libxml2=2.13.4=hb346dea_2
+libxslt=1.1.39=h76b75d6_0
+libzlib=1.3.1=hb9d3cd8_2
+llvmlite=0.43.0=py311h9c9ff8c_1
+locket=1.0.0=pyhd8ed1ab_0
+lxml=5.3.0=py311hcfaa980_2
+lz4=4.3.3=py311h2cbdf9a_1
+lz4-c=1.9.4=hcb278e6_0
+markupsafe=3.0.2=py311h2dc5d0c_0
+matplotlib-base=3.9.2=py311h2b939e6_1
+matplotlib-inline=0.1.7=pypi_0
+mpc=1.3.1=h24ddda3_1
+mpfr=4.2.1=h90cbb55_3
+mpmath=1.3.0=pyhd8ed1ab_0
+msgpack-python=1.1.0=py311hd18a35c_0
+munkres=1.1.4=pyh9f0ad1d_0
+ncurses=6.5=he02047a_1
+nest-asyncio=1.6.0=pyhd8ed1ab_0
+networkx=3.4.2=pyhd8ed1ab_1
+numba=0.60.0=py311h4bc866e_0
+numpy=1.26.4=pypi_0
+openjpeg=2.5.2=h488ebb8_0
+openpyxl=3.1.5=pypi_0
+openssl=3.3.2=hb9d3cd8_0
+opgee=4.0a0=dev_0
+orc=2.0.2=h690cf93_1
+packaging=24.1=pyhd8ed1ab_0
+pandas=2.2.3=py311h7db5c69_1
+pango=1.54.0=h4c5309f_1
+parso=0.8.4=pypi_0
+partd=1.4.2=pyhd8ed1ab_0
+pcre2=10.44=hba22ea6_2
+pexpect=4.9.0=pypi_0
+pillow=11.0.0=py311h49e9ac3_0
+pint=0.24.3=pyhd8ed1ab_0
+pint-pandas=0.6.2=pyhd8ed1ab_0
+pip=24.3.1=pyh8b19718_0
+pixman=0.43.2=h59595ed_0
+plotly=5.24.1=pyhd8ed1ab_0
+pluggy=1.5.0=pyhd8ed1ab_0
+prompt-toolkit=3.0.48=pypi_0
+psutil=6.1.0=py311h9ecbd09_0
+pthread-stubs=0.4=hb9d3cd8_1002
+ptyprocess=0.7.0=pypi_0
+pure-eval=0.2.3=pypi_0
+pyarrow=18.0.0=py311hbd00459_0
+pyarrow-core=18.0.0=py311h4854187_0_cpu
+pycparser=2.22=pyhd8ed1ab_0
+pydot=3.0.1=py311h38be061_1
+pyglet=2.0.18=pypi_0
+pygments=2.18.0=pyhd8ed1ab_0
+pyparsing=3.2.0=pyhd8ed1ab_1
+pysocks=1.7.1=pyha2e5f31_6
+pytest=8.3.3=pyhd8ed1ab_0
+python=3.11.10=hc5c86c4_3_cpython
+python-dateutil=2.9.0=pyhd8ed1ab_0
+python-levenshtein=0.26.1=pyhff2d567_0
+python-tzdata=2024.2=pyhd8ed1ab_0
+python_abi=3.11=5_cp311
+pytz=2024.1=pyhd8ed1ab_0
+pyxsteam=0.4.9=pypi_0
+pyyaml=6.0.2=py311h9ecbd09_1
+qhull=2020.2=h434a139_5
+rapidfuzz=3.10.1=py311hfdbb021_0
+re2=2024.07.02=h77b4e00_1
+readline=8.2=h8228510_1
+requests=2.32.3=pyhd8ed1ab_0
+retrying=1.3.3=pyhd8ed1ab_3
+s2n=1.5.5=h3931f03_0
+scipy=1.14.1=py311he9a78e4_1
+setuptools=75.3.0=pyhd8ed1ab_0
+six=1.16.0=pyh6c4a22f_0
+snappy=1.2.1=ha2e4443_0
+snowballstemmer=2.2.0=pyhd8ed1ab_0
+sortedcontainers=2.4.0=pyhd8ed1ab_0
+sphinx=8.1.3=pyhd8ed1ab_0
+sphinx-argparse=0.5.2=pyhd8ed1ab_0
+sphinx_rtd_theme=3.0.1=pyha770c72_0
+sphinxcontrib-applehelp=2.0.0=pyhd8ed1ab_0
+sphinxcontrib-devhelp=2.0.0=pyhd8ed1ab_0
+sphinxcontrib-htmlhelp=2.1.0=pyhd8ed1ab_0
+sphinxcontrib-jquery=4.1=pyhd8ed1ab_0
+sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
+sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_0
+sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_0
+stack-data=0.6.3=pypi_0
+sympy=1.13.3=pyh2585a3b_104
+tblib=3.0.0=pyhd8ed1ab_0
+tenacity=9.0.0=pyhd8ed1ab_0
+thermo=0.3.0=pyhd8ed1ab_0
+thermosteam=0.45.0=pypi_0
+tk=8.6.13=noxft_h4845f30_101
+tomli=2.0.2=pyhd8ed1ab_0
+toolz=1.0.0=pyhd8ed1ab_0
+tornado=6.4.1=py311h9ecbd09_1
+traitlets=5.14.3=pypi_0
+typing-extensions=4.12.2=hd8ed1ab_0
+typing_extensions=4.12.2=pyha770c72_0
+tzdata=2024b=hc8b5060_0
+unicodedata2=15.1.0=py311h9ecbd09_1
+urllib3=2.2.3=pyhd8ed1ab_0
+wcwidth=0.2.13=pypi_0
+werkzeug=3.0.6=pypi_0
+wheel=0.44.0=pyhd8ed1ab_0
+xlrd=2.0.1=pypi_0
+xorg-libice=1.1.1=hb9d3cd8_1
+xorg-libsm=1.2.4=he73a12e_1
+xorg-libx11=1.8.10=h4f16b4b_0
+xorg-libxau=1.0.11=hb9d3cd8_1
+xorg-libxdmcp=1.1.5=hb9d3cd8_0
+xorg-libxext=1.3.6=hb9d3cd8_0
+xorg-libxrender=0.9.11=hb9d3cd8_1
+xorg-xorgproto=2024.1=hb9d3cd8_1
+xyzservices=2024.9.0=pyhd8ed1ab_0
+xz=5.2.6=h166bdaf_0
+yaml=0.2.5=h7f98852_2
+zict=3.0.0=pyhd8ed1ab_0
+zipp=3.20.2=pyhd8ed1ab_0
+zlib=1.3.1=hb9d3cd8_2
+zstandard=0.23.0=py311hbc35293_1
+zstd=1.5.6=ha6fb4c9_0
diff --git a/py3-opgee-unix.yml b/py3-opgee-unix.yml
index 0fd0578d..1c4ecb90 100644
--- a/py3-opgee-unix.yml
+++ b/py3-opgee-unix.yml
@@ -1,15 +1,14 @@
 name: opgee
 channels:
-  - anaconda
   - conda-forge
   - defaults
+channel_priority: strict
 dependencies:
-  - colour
+  - chemicals
   - dash
   - dask
   - dask-jobqueue
-  - jinja2
-  - llvm-openmp
+  - fluids
   - lxml
   - networkx
   - numba
@@ -21,18 +20,14 @@ dependencies:
   - pydot
   - pytest
   - python>=3.11.0,<3.12.0
-  - semver
   - setuptools
   - sphinx
   - sphinx-argparse
   - sphinx_rtd_theme
   - sphinxcontrib-serializinghtml
+  - thermo
   - pip:
-    # - nuitka            # experimental; moved here because conda version is very outdated
-    - chemicals
     - dash-cytoscape
-    - fluids
     - pyXSteam
-    - thermo
     - thermosteam
 
diff --git a/py3-opgee-win10.yml b/py3-opgee-win10.yml
index ea4f01e0..fbc0f7bf 100644
--- a/py3-opgee-win10.yml
+++ b/py3-opgee-win10.yml
@@ -11,7 +11,6 @@ dependencies:
   - jinja2
   - llvm-openmp
   - lxml
-  - llvmlite
   - networkx
   - numba
   - numpy
diff --git a/requirements.txt b/requirements.txt
index 89e0d702..8d569658 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,27 +1,28 @@
 # This file was generated by the script update-reqs.py. Manual edits may be lost.
 chemicals==1.2.0
-dash==2.14.2
+dash==2.18.1
+dash-core-components==2.0.0
 dash-cytoscape==1.0.2
-dask==2024.8.2
-dask-jobqueue==0.8.2
+dash-html-components==2.0.0
+dash-table==5.0.0
+dask==2024.10.0
+dask-jobqueue==0.9.0
 fluids==1.0.26
-future==0.18.3
-lxml==5.2.1
-matplotlib==3.9.2
-networkx==3.2.1
+future==1.0.0
+lxml==5.3.0
+networkx==3.4.2
 numpy==1.26.4
-pandas==2.2.2
+pandas==2.2.3
 pint==0.24.3
 pint-pandas==0.6.2
-pydot==1.4.2
-pytest==7.4.4
-python-dateutil==2.9.0post0
+pydot==3.0.1
+pytest==8.3.3
+python-dateutil==2.9.0
 pyxsteam==0.4.9
 scipy==1.14.1
-semver==3.0.2
-setuptools==75.1.0
-sphinx==7.3.7
+setuptools==75.3.0
+sphinx==8.1.3
 sphinx-argparse==0.5.2
-sphinx_rtd_theme==2.0.0
+sphinx_rtd_theme==3.0.1
 thermo==0.3.0
 thermosteam==0.45.0
diff --git a/update-reqs.py b/update-reqs.py
index 61f60703..4ca43637 100755
--- a/update-reqs.py
+++ b/update-reqs.py
@@ -18,7 +18,7 @@ def main():
         pkgs = [line.strip() for line in f.readlines() if not line.startswith('#')]
 
     expr = '(' + '|'.join(pkgs) + ')'
-    cmd = f"conda list -n opgee | egrep -v '^#' | egrep '^{expr}\s+'"
+    cmd = f"conda list -n opgee | egrep -v '^#' | egrep '^{expr}\\s+'"
 
     if Verbose:
         print(cmd)

From 4e6a6c93498160e12aeaa2fc0dddeba77a8f1453 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 21:42:34 -0600
Subject: [PATCH 07/20] unify conda envs

---
 py3-opgee-unix.yml => py3-opgee-all.yml |  0
 py3-opgee-win10.yml                     | 36 -------------------------
 2 files changed, 36 deletions(-)
 rename py3-opgee-unix.yml => py3-opgee-all.yml (100%)
 delete mode 100644 py3-opgee-win10.yml

diff --git a/py3-opgee-unix.yml b/py3-opgee-all.yml
similarity index 100%
rename from py3-opgee-unix.yml
rename to py3-opgee-all.yml
diff --git a/py3-opgee-win10.yml b/py3-opgee-win10.yml
deleted file mode 100644
index fbc0f7bf..00000000
--- a/py3-opgee-win10.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-name: opgee
-channels:
-  - anaconda
-  - conda-forge
-  - defaults
-dependencies:
-  - colour
-  - dash
-  - dask
-  - dask-jobqueue
-  - jinja2
-  - llvm-openmp
-  - lxml
-  - networkx
-  - numba
-  - numpy
-  - pandas
-  - pint
-  - pint-pandas
-  - pip
-  - pydot
-  - pytest
-  - python>=3.9.0,<3.10.0
-  - semver
-  - setuptools
-  - sphinx
-  - sphinx-argparse
-  - sphinx_rtd_theme
-  - sphinxcontrib-serializinghtml
-  - thermo
-  - fluids
-  - chemicals
-  - pip:
-    - thermosteam
-    - pyXSteam
-    - dash-cytoscape
\ No newline at end of file

From 0611f56f558110be6b1d3947fbf592263f0729b0 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 21:44:46 -0600
Subject: [PATCH 08/20] remove arch from matrix, "macos-latest" curretly uses
 M1

---
 .github/workflows/opgee-test.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index 67107c6e..9f415e8c 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -10,13 +10,7 @@ jobs:
   test:
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        arch: [x64, arm64]
-        exclude:
-          - os: ubuntu-latest
-            arch: arm64
-          - os: macos-latest
-            arch: x64
+        os: [ubuntu-latest, macos-latest, windows-latest]
       max-parallel: 5
     runs-on: ${{ matrix.os }}
     defaults:

From b1344a6a28cda6f4e4fae310e4777ec111cb7789 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 21:49:01 -0600
Subject: [PATCH 09/20] rename env file

---
 .github/workflows/opgee-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index 9f415e8c..fcede888 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -20,7 +20,7 @@ jobs:
       OPGEE_HOME: ${{ github.workspace }}/tests/files
       CI: 'true'
       opgee_pkg_list: 'opgee.pkg_list.txt'
-      opgee_env_yml: 'py3-opgee-unix.yml'
+      opgee_env_yml: 'py3-opgee-all.yml'
     steps:
     - uses: actions/checkout@v4
     - name: Cache pip dependencies

From cfc0acfa1ca2e26f6b698e50e5b6204f0175243d Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Fri, 1 Nov 2024 22:02:01 -0600
Subject: [PATCH 10/20] remove channel priority

---
 py3-opgee-all.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/py3-opgee-all.yml b/py3-opgee-all.yml
index 1c4ecb90..e3d3c680 100644
--- a/py3-opgee-all.yml
+++ b/py3-opgee-all.yml
@@ -2,7 +2,6 @@ name: opgee
 channels:
   - conda-forge
   - defaults
-channel_priority: strict
 dependencies:
   - chemicals
   - dash

From 5f736285bd62f793cf0a984e41ba3ee78d399ed7 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 17:53:01 -0700
Subject: [PATCH 11/20] fix failing windows test

---
 tests/test_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_config.py b/tests/test_config.py
index 31b7af6a..be7b1740 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -29,7 +29,7 @@ def test_realpath(tmp_path):    # built-in fixture returns a temporary directory
 
     bar = tmp_path / 'bar.txt'
     os.symlink(foo, bar)
-    assert pathjoin(bar, realpath=True) == str(foo)
+    assert pathjoin(bar, realpath=True) == unixPath(str(foo))
 
 
 def test_reload():

From c030ae3af60d56c7fdd937d73eb9a0524d984144 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 17:55:44 -0700
Subject: [PATCH 12/20] rename env yml

---
 py3-opgee-all.yml => py3-opgee.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename py3-opgee-all.yml => py3-opgee.yml (100%)

diff --git a/py3-opgee-all.yml b/py3-opgee.yml
similarity index 100%
rename from py3-opgee-all.yml
rename to py3-opgee.yml

From f2a796d5f729a41cc63d002665aa3dc2ff4080c1 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 17:57:47 -0700
Subject: [PATCH 13/20] fix env name ref

---
 .github/workflows/opgee-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index fcede888..7f0bc729 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -20,7 +20,7 @@ jobs:
       OPGEE_HOME: ${{ github.workspace }}/tests/files
       CI: 'true'
       opgee_pkg_list: 'opgee.pkg_list.txt'
-      opgee_env_yml: 'py3-opgee-all.yml'
+      opgee_env_yml: 'py3-opgee.yml'
     steps:
     - uses: actions/checkout@v4
     - name: Cache pip dependencies

From 2d7290f26fd47eac7b81fdaaeb6e279e99093d07 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 18:02:10 -0700
Subject: [PATCH 14/20] fix conditional

---
 .github/workflows/opgee-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index 7f0bc729..da42ff35 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -53,6 +53,6 @@ jobs:
         conda env update -n opgee -f $opgee_env_yml
         pip install -e .
         pip install pytest-cov codecov coveralls PyYAML
-      if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.cache-hit != 'true'
+      if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.outputs.cache-hit != 'true'
     - name: Run unit tests with coverage
       run: coverage run --source=opgee -m pytest

From 4eb3bfff544ffaf7835a1f8ff4dd1be9a1a4519c Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 18:14:13 -0700
Subject: [PATCH 15/20] add conda package caching

---
 .github/workflows/opgee-test.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index da42ff35..ae9f5253 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -23,6 +23,14 @@ jobs:
       opgee_env_yml: 'py3-opgee.yml'
     steps:
     - uses: actions/checkout@v4
+    - name: Cache Conda packages
+      uses: actions/cache@v3
+      env:
+        CACHE_NUMBER: 0
+      with:
+        enableCrossOsArchive: true
+        path: ${{ runner.os == 'Windows' && 'D:\conda_pkgs_dir' || '~/conda_pkgs_dir'}}
+        key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(env.opgee_env_yml) }}
     - name: Cache pip dependencies
       uses: actions/cache@v3
       id: pip-cache

From f4cc72483284e9fe72860899f77b425a8301f555 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 18:23:23 -0700
Subject: [PATCH 16/20] fix formatting, add cross os caching

---
 .github/workflows/opgee-test.yml | 90 ++++++++++++++++----------------
 1 file changed, 45 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index ae9f5253..bdf66860 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -18,49 +18,49 @@ jobs:
         shell: bash -el {0}
     env:
       OPGEE_HOME: ${{ github.workspace }}/tests/files
-      CI: 'true'
-      opgee_pkg_list: 'opgee.pkg_list.txt'
-      opgee_env_yml: 'py3-opgee.yml'
+      CI: "true"
+      opgee_pkg_list: "opgee.pkg_list.txt"
+      opgee_env_yml: "py3-opgee.yml"
     steps:
-    - uses: actions/checkout@v4
-    - name: Cache Conda packages
-      uses: actions/cache@v3
-      env:
-        CACHE_NUMBER: 0
-      with:
-        enableCrossOsArchive: true
-        path: ${{ runner.os == 'Windows' && 'D:\conda_pkgs_dir' || '~/conda_pkgs_dir'}}
-        key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(env.opgee_env_yml) }}
-    - name: Cache pip dependencies
-      uses: actions/cache@v3
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key:
-          ${{ runner.os }}-pip-${{ hashFiles('requirements.txt')}}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-    - name: Init Anaconda
-      uses: conda-incubator/setup-miniconda@v3
-      with: 
-        miniforge-version: latest
-        activate-environment: opgee
-        python-version: 3.9
-    - name: Cache OPGEE env
-      id: opgee-env-cache
-      uses: actions/cache@v3
-      env:
-        # increment cache number to invalidate and rebuild the env
-        CACHE_NUMBER: 0
-      with:
-        path: ${{ env.CONDA }}/envs
-        key:
-          ${{ runner.os }}-conda-${{ runner.arch }}-${{ hashFiles(env.opgee_pkg_list) }}-${{ env.CACHE_NUMBER }}
-    - name: Update Conda env and pip dependencies
-      run: |
-        conda env update -n opgee -f $opgee_env_yml
-        pip install -e .
-        pip install pytest-cov codecov coveralls PyYAML
-      if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.outputs.cache-hit != 'true'
-    - name: Run unit tests with coverage
-      run: coverage run --source=opgee -m pytest
+      - uses: actions/checkout@v4
+      - name: Cache Conda packages
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 0
+        with:
+          enableCrossOsArchive: true
+          path: ${{ runner.os == 'Windows' && 'D:\conda_pkgs_dir' || '~/conda_pkgs_dir'}}
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(env.opgee_env_yml) }}
+      - name: Cache pip dependencies
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          enableCrossOsArchive: true
+          path: ${{ runner.os == 'Windows' && 'D:\.cache\pp' || '~/.cache/pip' }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt')}}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Init Anaconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          activate-environment: opgee
+          python-version: 3.9
+      - name: Cache OPGEE env
+        id: opgee-env-cache
+        uses: actions/cache@v3
+        env:
+          # increment cache number to invalidate and rebuild the env
+          CACHE_NUMBER: 0
+        with:
+          enableCrossOsArchive: true
+          path: ${{ env.CONDA }}/envs
+          key: ${{ runner.os }}-conda-${{ runner.arch }}-${{ hashFiles(env.opgee_pkg_list) }}-${{ env.CACHE_NUMBER }}
+      - name: Update Conda env and pip dependencies
+        run: |
+          conda env update -n opgee -f $opgee_env_yml
+          pip install -e .
+          pip install pytest-cov codecov coveralls PyYAML
+        if: steps.pip-cache.outputs.cache-hit != 'true' || steps.opgee-env-cache.outputs.cache-hit != 'true'
+      - name: Run unit tests with coverage
+        run: coverage run --source=opgee -m pytest

From 2667cd10a608e711de917d349c1f8c952d90619f Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Sun, 3 Nov 2024 18:40:42 -0700
Subject: [PATCH 17/20] fix pip cache path, update cache action version

---
 .github/workflows/opgee-test.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/opgee-test.yml b/.github/workflows/opgee-test.yml
index bdf66860..d9f409b9 100644
--- a/.github/workflows/opgee-test.yml
+++ b/.github/workflows/opgee-test.yml
@@ -24,19 +24,21 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Cache Conda packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           CACHE_NUMBER: 0
         with:
           enableCrossOsArchive: true
           path: ${{ runner.os == 'Windows' && 'D:\conda_pkgs_dir' || '~/conda_pkgs_dir'}}
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles(env.opgee_env_yml) }}
+          restore-keys: |
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-
       - name: Cache pip dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: pip-cache
         with:
           enableCrossOsArchive: true
-          path: ${{ runner.os == 'Windows' && 'D:\.cache\pp' || '~/.cache/pip' }}
+          path: ${{ runner.os == 'Windows' && 'D:\.cache\pip' || runner.os == 'macOS' && '~/Library/Caches/pip' || '~/.cache/pip' }}
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt')}}
           restore-keys: |
             ${{ runner.os }}-pip-
@@ -48,7 +50,7 @@ jobs:
           python-version: 3.9
       - name: Cache OPGEE env
         id: opgee-env-cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           # increment cache number to invalidate and rebuild the env
           CACHE_NUMBER: 0

From d05fdd21052b84203c96b24325e4cc323d4beb74 Mon Sep 17 00:00:00 2001
From: Richard Plevin <rich@plevin.com>
Date: Fri, 1 Nov 2024 09:38:32 -0700
Subject: [PATCH 18/20] Modified field graph to have arrowheads and stream
 content names. (Added on this branch owing to updated python env that only
 works in this branch currently!)

---
 opgee/graph.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/opgee/graph.py b/opgee/graph.py
index c5d39ad7..ff6e627f 100644
--- a/opgee/graph.py
+++ b/opgee/graph.py
@@ -91,13 +91,15 @@ def add_tree(graph, obj, level):
     display_in_notebook(graph)
 
 def write_process_diagram(field, pathname):
-    graph = pydot.Dot('model', graph_type='graph', bgcolor='white')
+    graph = pydot.Dot('model', graph_type='digraph', bgcolor='white')
 
     for name, proc in field.process_dict.items():
         graph.add_node(pydot.Node(name, shape='box'))
 
     for name, stream in field.stream_dict.items():
-        graph.add_edge(pydot.Edge(stream.src_name, stream.dst_name, color='black'))
+        contents = ', '.join(stream.contents)
+        graph.add_edge(pydot.Edge(stream.src_name, stream.dst_name,
+                                  color='black', label=contents))
 
     _logger.info(f"Writing {pathname}")
     graph.write_png(pathname)

From 7d4439e24927b08c63ba5d77d95904b16da1f6cd Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Mon, 4 Nov 2024 15:42:45 -0700
Subject: [PATCH 19/20] update opgee env file name

---
 Makefile | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index e5658ec1..33ab2287 100644
--- a/Makefile
+++ b/Makefile
@@ -65,14 +65,7 @@ travis-reqs $(TRAVIS_REQS): requirements.in
 #
 # Virtual environment / package dependency support
 #
-UNAME=$(strip $(shell uname))
-ifeq ($(UNAME), Darwin)
-	YML_FILE=py3-opgee-unix.yml
-else ifeq ($(UNAME), Linux)
-	YML_FILE=py3-opgee-unix.yml
-else
-	YML_FILE=py3-opgee-win10.yml
-endif
+YML_FILE=py3-opgee.yml
 
 
 #INPUT_YML=py3-opgee-macos.yml

From dd60959feaa00b78a4d27d6a0a2058301c273817 Mon Sep 17 00:00:00 2001
From: Michael Barlow <mbarlow@rmi.org>
Date: Mon, 4 Nov 2024 15:43:06 -0700
Subject: [PATCH 20/20] pkg list update

---
 opgee.pkg_list.txt | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/opgee.pkg_list.txt b/opgee.pkg_list.txt
index fca28feb..a051cd1e 100644
--- a/opgee.pkg_list.txt
+++ b/opgee.pkg_list.txt
@@ -8,19 +8,19 @@ ansicolors=1.1.8=pypi_0
 appdirs=1.4.4=pyh9f0ad1d_0
 asttokens=2.4.1=pypi_0
 atk-1.0=2.38.0=h04ea711_2
-aws-c-auth=0.7.31=hcdce11a_5
-aws-c-cal=0.7.4=hd3f4568_4
+aws-c-auth=0.8.0=h56a2c13_4
+aws-c-cal=0.8.0=hd3f4568_0
 aws-c-common=0.9.31=hb9d3cd8_0
-aws-c-compression=0.2.19=hf20e7d7_4
-aws-c-event-stream=0.5.0=h72d8268_0
-aws-c-http=0.8.10=h6bb76cc_5
-aws-c-io=0.14.20=h389d861_2
-aws-c-mqtt=0.10.7=had056f2_5
-aws-c-s3=0.7.0=hc85afc5_0
-aws-c-sdkutils=0.1.19=hf20e7d7_6
-aws-checksums=0.1.20=hf20e7d7_3
-aws-crt-cpp=0.29.0=h07ed512_0
-aws-sdk-cpp=1.11.407=h9c41b47_6
+aws-c-compression=0.3.0=hf20e7d7_0
+aws-c-event-stream=0.5.0=h68c3b0c_2
+aws-c-http=0.9.0=hfad4ed3_3
+aws-c-io=0.15.0=h17eb868_2
+aws-c-mqtt=0.11.0=h407ecb8_2
+aws-c-s3=0.7.0=hadeddc1_5
+aws-c-sdkutils=0.2.0=hf20e7d7_0
+aws-checksums=0.2.0=hf20e7d7_0
+aws-crt-cpp=0.29.0=h73f0fd4_6
+aws-sdk-cpp=1.11.407=h6a6dca0_6
 azure-core-cpp=1.14.0=h5cfcd09_0
 azure-identity-cpp=1.10.0=h113e628_0
 azure-storage-blobs-cpp=12.13.0=h3cf044e_1
@@ -115,10 +115,10 @@ ld_impl_linux-64=2.43=h712a8e2_2
 lerc=4.0.0=h27087fc_0
 levenshtein=0.26.1=py311hfdbb021_0
 libabseil=20240722.0=cxx17_h5888daf_1
-libarrow=18.0.0=ha5db6c2_0_cpu
-libarrow-acero=18.0.0=h5888daf_0_cpu
-libarrow-dataset=18.0.0=h5888daf_0_cpu
-libarrow-substrait=18.0.0=he882d9a_0_cpu
+libarrow=18.0.0=ha5db6c2_1_cpu
+libarrow-acero=18.0.0=h5888daf_1_cpu
+libarrow-dataset=18.0.0=h5888daf_1_cpu
+libarrow-substrait=18.0.0=h5c8f2c3_1_cpu
 libblas=3.9.0=25_linux64_openblas
 libbrotlicommon=1.1.0=hb9d3cd8_2
 libbrotlidec=1.1.0=hb9d3cd8_2
@@ -140,9 +140,9 @@ libgfortran-ng=14.2.0=h69a702a_1
 libgfortran5=14.2.0=hd5240d6_1
 libglib=2.82.2=h2ff4ddf_0
 libgomp=14.2.0=h77fa898_1
-libgoogle-cloud=2.30.0=h438788a_0
-libgoogle-cloud-storage=2.30.0=h0121fbd_0
-libgrpc=1.65.5=hf5c653b_0
+libgoogle-cloud=2.30.0=h804f50b_1
+libgoogle-cloud-storage=2.30.0=h0121fbd_1
+libgrpc=1.67.1=hc2c308b_0
 libiconv=1.17=hd590300_2
 libjpeg-turbo=3.0.0=hd590300_1
 liblapack=3.9.0=25_linux64_openblas
@@ -150,9 +150,9 @@ libllvm14=14.0.6=hcd5def8_4
 libnghttp2=1.64.0=h161d5f1_0
 libnsl=2.0.1=hd590300_0
 libopenblas=0.3.28=pthreads_h94d23a6_0
-libparquet=18.0.0=h6bd9018_0_cpu
+libparquet=18.0.0=h6bd9018_1_cpu
 libpng=1.6.44=hadc24fc_0
-libprotobuf=5.27.5=h5b01275_2
+libprotobuf=5.28.2=h5b01275_0
 libre2-11=2024.07.02=hbbce691_1
 librsvg=2.58.4=hc0ffecb_0
 libsqlite=3.47.0=hadc24fc_1
@@ -191,7 +191,7 @@ openjpeg=2.5.2=h488ebb8_0
 openpyxl=3.1.5=pypi_0
 openssl=3.3.2=hb9d3cd8_0
 opgee=4.0a0=dev_0
-orc=2.0.2=h690cf93_1
+orc=2.0.2=he039a57_2
 packaging=24.1=pyhd8ed1ab_0
 pandas=2.2.3=py311h7db5c69_1
 pango=1.54.0=h4c5309f_1
@@ -234,7 +234,7 @@ re2=2024.07.02=h77b4e00_1
 readline=8.2=h8228510_1
 requests=2.32.3=pyhd8ed1ab_0
 retrying=1.3.3=pyhd8ed1ab_3
-s2n=1.5.5=h3931f03_0
+s2n=1.5.6=h0e56266_0
 scipy=1.14.1=py311he9a78e4_1
 setuptools=75.3.0=pyhd8ed1ab_0
 six=1.16.0=pyh6c4a22f_0