Merge branch 'master' into outbands

.github/workflows/tests.yaml

@@ -28,7 +28,7 @@ jobs:
       - name: Get SOCRATES
         uses: actions/checkout@v4
         with:
-          repository: 'FormingWorlds/SOCRATES'
+          repository: 'nichollsh/SOCRATES'
           path: 'SOCRATES'
 
       - uses: actions/cache@v3

CONTRIBUTING.md

@@ -42,14 +42,14 @@ The versioning scheme we use is [CalVer](https://calver.org/).
 0. Update requirements files:
 
 ```console
-python tools/requirements_txt.py
+python tools/generate_requirements_txt.py
 pip-compile -o requirements_full.txt pyproject.toml
 ```
 
 1. Bump the version (`release`/`patch`) as needed
 
 ```console
-bump-my-version release
+bump-my-version bump release
 # 24.06.26
 ```
 

README.md

@@ -30,7 +30,7 @@ https://proteus-code.readthedocs.io
 ### Developer installation instructions
 1. Download and install Socrates
 ```console
-git clone [email protected]:FormingWorlds/SOCRATES.git
+git clone [email protected]:nichollsh/SOCRATES.git
 cd SOCRATES
 ./configure
 ./build-code
@@ -50,7 +50,7 @@ pip install -e .
         * `janus download spectral`
         * `janus download stellar`
     * Alternatively, you can specify which spectral data you want to download, and optionally the number of bands
-        * `janus download spectral /Frostflow 4096`
+        * `janus download spectral -n Frostflow -b 4096`
 
 ### Run instructions
 In the examples folder you can find python scripts showing typical usecases/workflows of atmosphere modelling with Janus.

examples/requirements.txt

@@ -0,0 +1,2 @@
+fwl-janus
+fwl-mors

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fwl-janus"
-version = "24.06.26"
+version = "24.08.29"
 description = "Temperature structure generator for planetory atmospheres."
 readme = "README.md"
 authors = [
@@ -41,7 +41,6 @@ dependencies = [
   'toml',
   'tomlkit',
   'f90nml',
-  'fwl-mors',
 ]
 
 [project.urls]
@@ -51,6 +50,7 @@ homepage = "https://github.com/FormingWorlds/JANUS"
 develop = [
   "bump-my-version",
   "coverage[toml]",
+  'fwl-mors',
   "pytest"
 ]
 docs = [
@@ -81,7 +81,7 @@ testpaths = ["tests"]
 
 [tool.bumpversion]
 # https://callowayproject.github.io/bump-my-version/howtos/calver/
-current_version = "24.06.26"
+current_version = "24.08.29"
 parse = """(?x)                     # Verbose mode
     (?P<release>                    # The release part
         (?:[1-9][0-9])\\.           # YY.

requirements.txt

@@ -1,9 +1,13 @@
 # generated by tools/generate_requirements_txt.py
+click
 matplotlib
 natsort
 netcdf4
 numpy
+osfclient
 pandas
+platformdirs
+requests
 scipy
 seaborn
 toml

requirements_full.txt

@@ -5,9 +5,15 @@
 #    pip-compile --output-file=requirements_full.txt pyproject.toml
 #
 certifi==2024.6.2
-    # via netcdf4
+    # via
+    #   netcdf4
+    #   requests
 cftime==1.6.4
     # via netcdf4
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via fwl-janus (pyproject.toml)
 contourpy==1.2.1
     # via matplotlib
 cycler==0.12.1
@@ -16,6 +22,8 @@ f90nml==1.4.4
     # via fwl-janus (pyproject.toml)
 fonttools==4.53.0
     # via matplotlib
+idna==3.8
+    # via requests
 kiwisolver==1.4.5
     # via matplotlib
 matplotlib==3.9.0
@@ -36,6 +44,8 @@ numpy==2.0.0
     #   pandas
     #   scipy
     #   seaborn
+osfclient==0.0.5
+    # via fwl-janus (pyproject.toml)
 packaging==24.1
     # via matplotlib
 pandas==2.2.2
@@ -44,6 +54,8 @@ pandas==2.2.2
     #   seaborn
 pillow==10.3.0
     # via matplotlib
+platformdirs==4.2.2
+    # via fwl-janus (pyproject.toml)
 pyparsing==3.1.2
     # via matplotlib
 python-dateutil==2.9.0.post0
@@ -52,15 +64,25 @@ python-dateutil==2.9.0.post0
     #   pandas
 pytz==2024.1
     # via pandas
+requests==2.32.3
+    # via
+    #   fwl-janus (pyproject.toml)
+    #   osfclient
 scipy==1.14.0
     # via fwl-janus (pyproject.toml)
 seaborn==0.13.2
     # via fwl-janus (pyproject.toml)
 six==1.16.0
-    # via python-dateutil
+    # via
+    #   osfclient
+    #   python-dateutil
 toml==0.10.2
     # via fwl-janus (pyproject.toml)
 tomlkit==0.12.5
     # via fwl-janus (pyproject.toml)
+tqdm==4.66.5
+    # via osfclient
 tzdata==2024.1
     # via pandas
+urllib3==2.2.2
+    # via requests

src/janus/set_socrates_env.py

@@ -1,7 +1,7 @@
 """Import this file to set environment variables for socrates.
 
 Based on:
-https://github.com/FormingWorlds/SOCRATES/blob/main/sbin/set_rad_env_tmp
+https://github.com/nichollsh/SOCRATES/blob/main/sbin/set_rad_env_tmp
 """
 
 from __future__ import annotations

src/janus/utils/atmosphere_column.py

@@ -321,7 +321,7 @@ def setPlanetProperties(self, pl_radius:float, pl_mass:float):
     def setVolatiles(self, vol_mixing: dict):
 
         tot_mixing =  float(sum(vol_mixing.values()))  # Ensure mixing ratios add up to unity
-        self.vol_list = {key: val/tot_mixing for key, val in self.vol_mixing.items()}
+        self.vol_list = {key: val/tot_mixing for key, val in vol_mixing.items()}
 
         # H2O floor to prevent NaNs
         self.vol_list["H2O"] = np.max( [ self.vol_list["H2O"], 1e-20 ] )