PySDM 2.93__tar.gz → 2.95__tar.gz

{pysdm-2.93 → pysdm-2.95}/.github/workflows/pdoc.yml

@@ -27,21 +27,15 @@ jobs:
         with:
           python-version: "3.12"
       - run: |
-          pip install pdoc nbformat
+          pip install pdoc nbformat gitpython
           pip install -e .
           pip install -e examples
 
-          python - <<EOF
-          import glob, nbformat
-          for notebook_path in glob.glob('examples/PySDM_examples/*/*.ipynb'):
-            with open(notebook_path, encoding="utf8") as fin:
-              with open(notebook_path + ".badges.md", 'w') as fout:
-                fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source)
-          EOF
-          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PySDM examples/PySDM_examples -t docs/templates --math --mermaid
+          python -We docs/generate_html.py . .
+        
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
         uses: JamesIves/github-pages-deploy-action@4.1.1
         with:
           branch: pdoc
           folder: html
-          clean: true
+          clean: true

{pysdm-2.93 → pysdm-2.95}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.93
+Version: 2.95
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors

{pysdm-2.93 → pysdm-2.95}/PySDM/backends/impl_numba/methods/chemistry_methods.py

@@ -234,8 +234,8 @@ class ChemistryMethods(BackendMethods):
             SO2aq = moles_S_IV[i] / droplet_volume[i] / dissociation_factor_SO2[i]
 
             # NB: This might not be entirely correct
-            # https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/JD092iD04p04171
-            # https://www.atmos-chem-phys.net/16/1693/2016/acp-16-1693-2016.pdf
+            # https://doi.org/10.1029/JD092iD04p04171
+            # https://doi.org/10.5194/acp-16-1693-2016
 
             ozone = (
                 (

{pysdm-2.93 → pysdm-2.95}/PySDM/dynamics/collisions/breakup_fragmentations/feingold1988.py

@@ -1,7 +1,7 @@
 """
 P(m; x, y) = nu^2 * (x+y) exp(-m * nu)
 nu = 1/m* where m* is a scaling factor for fragment volume dist.
-see [Feingold et al. 1999](https://doi.org/10.1175/1520-0469(1999)056<4100:TIOGCC>2.0.CO;2)
+see [Feingold et al. 1999](https://doi.org/10.1175/1520-0469(1999)056%3C4100:TIOGCC%3E2.0.CO;2)
 """
 
 from .impl import VolumeBasedFragmentationFunction

{pysdm-2.93 → pysdm-2.95}/PySDM/dynamics/collisions/breakup_fragmentations/lowlist82.py

@@ -1,5 +1,5 @@
 """
-See [Low & List 1982](https://doi.org/10.1175/1520-0469(1982)039<1607:CCABOR>2.0.CO;2)
+See [Low & List 1982](https://doi.org/10.1175/1520-0469(1982)039%3C1607:CCABOR%3E2.0.CO;2)
 """
 
 from .impl import VolumeBasedFragmentationFunction

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/constants_defaults.py

@@ -193,7 +193,7 @@ STRAUB_MU2 = 0.095 * si.cm
 VEDDER_1987_b = 89 / 880
 VEDDER_1987_A = 993 / 880 / 3 / VEDDER_1987_b
 
-""" [eq. 5 in Merlivat and Nief (1967)](https://doi.org/10.3402/tellusa.v19i1.9756) """
+""" [eq. 5 in Merlivat and Nief 1967](https://doi.org/10.3402/tellusa.v19i1.9756) """
 MERLIVAT_NIEF_1967_ALPHA_L_2H_T2 = 15013 * si.K**2
 MERLIVAT_NIEF_1967_ALPHA_L_2H_T1 = 0 * si.K
 MERLIVAT_NIEF_1967_ALPHA_L_2H_T0 = -0.1
@@ -202,17 +202,17 @@ MERLIVAT_NIEF_1967_ALPHA_I_2H_T2 = 16289 * si.K**2
 MERLIVAT_NIEF_1967_ALPHA_I_2H_T1 = 0 * si.K
 MERLIVAT_NIEF_1967_ALPHA_I_2H_T0 = -0.0945
 
-""" [Lamb et al. (2017)](https://doi.org/10.1073/pnas.1618374114) """
+""" [Lamb et al. 2017](https://doi.org/10.1073/pnas.1618374114) """
 LAMB_ET_AL_2017_ALPHA_I_2H_T2 = 13525 * si.K**2
 LAMB_ET_AL_2017_ALPHA_I_2H_T1 = 0 * si.K
 LAMB_ET_AL_2017_ALPHA_I_2H_T0 = -0.0559
 
-""" [Ellehoj et al. (2013)](https://doi.org/10.1002/rcm.6668) """
+""" [Ellehoj et al. 2013](https://doi.org/10.1002/rcm.6668) """
 ELLEHOJ_ET_AL_2013_ALPHA_I_2H_T2 = 48888 * si.K**2
 ELLEHOJ_ET_AL_2013_ALPHA_I_2H_T1 = -203.1 * si.K
 ELLEHOJ_ET_AL_2013_ALPHA_I_2H_T0 = 0.2133
 
-""" [Majoube (1971)](https://doi.org/10.1051/jcp/1971681423) """
+""" [Majoube 1971](https://doi.org/10.1051/jcp/1971681423) """
 # values taken from Jouzel 1986 (eqs. 1)
 MAJOUBE_1971_ALPHA_L_18O_T2 = 1137 * si.K**2
 MAJOUBE_1971_ALPHA_L_18O_T1 = -0.4156 * si.K
@@ -223,12 +223,12 @@ MAJOUBE_1971_ALPHA_L_2H_T2 = 24844 * si.K**2
 MAJOUBE_1971_ALPHA_L_2H_T1 = -76.248 * si.K
 MAJOUBE_1971_ALPHA_L_2H_T0 = 0.052612
 
-""" [Majoube (1970)](https://doi.org/10.1038/2261242a0) """
+""" [Majoube 1970](https://doi.org/10.1038/2261242a0) """
 MAJOUBE_1970_ALPHA_I_18O_T2 = 0 * si.K**2
 MAJOUBE_1970_ALPHA_I_18O_T1 = 11.839 * si.K
 MAJOUBE_1970_ALPHA_I_18O_T0 = -0.028224
 
-""" [Van Hook (1968)](https://doi.org/10.1021/j100850a028) """
+""" [Van Hook 1968](https://doi.org/10.1021/j100850a028) """
 VAN_HOOK_1968_ALPHA_I_2H_A = 11484.5 * si.K**2
 VAN_HOOK_1968_ALPHA_I_2H_B = 35.3315 * si.K
 VAN_HOOK_1968_ALPHA_I_2H_C = -0.159290
@@ -285,7 +285,7 @@ VAN_HOOK_1968_ALPHA_L_DOD_A = 49314.9 * si.K**2
 VAN_HOOK_1968_ALPHA_L_DOD_B = -164.266 * si.K
 VAN_HOOK_1968_ALPHA_L_DOD_C = 0.140049
 
-""" [Horita and Wesolowski (1994)](https://doi.org/10.1016/0016-7037(94)90096-5) """
+""" [Horita and Wesolowski 1994](https://doi.org/10.1016/0016-7037(94)90096-5) """
 HORITA_AND_WESOLOWSKI_1994_ALPHA_L_18O_T3 = 1e-3 * 0.35041e9 * si.K**3
 HORITA_AND_WESOLOWSKI_1994_ALPHA_L_18O_T2 = 1e-3 * -1.6664e6 * si.K**2
 HORITA_AND_WESOLOWSKI_1994_ALPHA_L_18O_T1 = 1e-3 * 6.7123e3 * si.K
@@ -303,7 +303,7 @@ BARKAN_AND_LUZ_2005_EXPONENT = 0.529
 """ eq. 11 in [Barkan and Luz 2007](https://doi.org/10.1002/rcm.3180) """
 BARKAN_AND_LUZ_2007_EXCESS_18O_COEFF = 0.528
 
-""" [Craig 1961](https://doi.org/10.1126/science.133.3465.170) """
+""" [Craig 1961](https://doi.org/10.1126/science.133.3465.1702) """
 CRAIG_1961_SLOPE_COEFF = 8
 CRAIG_1961_INTERCEPT_COEFF = 10 * PER_MILLE
 
@@ -321,7 +321,7 @@ diffusion_thermics_K_G11_C = 1e-4 * si.W / si.m / si.K**2
 diffusion_thermics_K_G11_D = -3.9e-4 * si.W / si.m / si.K
 
 """
-[Pruppacher & Rasmussen (1979))](https://doi.org/10.1175/1520-0469(1979)036<1255:AWTIOT>2.0.CO;2)
+[Pruppacher & Rasmussen 1979](https://doi.org/10.1175/1520-0469(1979)036%3C1255:AWTIOT%3E2.0.CO;2)
 """
 PRUPPACHER_RASMUSSEN_1979_XTHRES = 1.4 * si.dimensionless
 PRUPPACHER_RASMUSSEN_1979_CONSTSMALL = 1.0 * si.dimensionless
@@ -330,7 +330,7 @@ PRUPPACHER_RASMUSSEN_1979_POWSMALL = 2 * si.dimensionless
 PRUPPACHER_RASMUSSEN_1979_CONSTBIG = 0.78 * si.dimensionless
 PRUPPACHER_RASMUSSEN_1979_COEFFBIG = 0.308 * si.dimensionless
 
-"""[Zografos et al. (1987)](https://doi.org/10.1016/0045-7825(87)90003-X) Table 1"""
+"""[Zografos et al. 1987](https://doi.org/10.1016/0045-7825(87)90003-X) Table 1"""
 ZOGRAFOS_1987_COEFF_T3 = 2.5914e-15 * si.K ** (-3) * si.Pa * si.s
 ZOGRAFOS_1987_COEFF_T2 = -1.4346e-11 * si.K ** (-2) * si.Pa * si.s
 ZOGRAFOS_1987_COEFF_T1 = 5.0523e-8 / si.K * si.Pa * si.s

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/isotope_equilibrium_fractionation_factors/van_hook_1968.py

@@ -1,5 +1,5 @@
 """
-Vapour pressure factors from Table V in [Van Hook 1968](https://10.1021/j100850a028)
+Vapour pressure factors from Table V in [Van Hook 1968](https://doi.org/10.1021/j100850a028)
 """
 
 import numpy as np

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/isotope_ratio_evolution/merlivat_and_jouzel_1979.py

@@ -1,7 +1,7 @@
 """
 see derivation of eq. (12) in [Merlivat and Jouzel 1979](https://doi.org/10.1029/JC084iC08p05029)
 (for constant alpha leads to eq. (13) in
-[Gedzelman & Arnold 1994](https://doi.org/10.1029/93jd03518))
+[Gedzelman & Arnold 1994](https://doi.org/10.1029/93JD03518))
 """
 
 

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/saturation_vapour_pressure/bolton_1980.py

@@ -1,5 +1,5 @@
 """
-[Bolton 1980](https://doi.org/10.1175/1520-0493(1980)108<1046:TCOEPT>2.0.CO;2)
+[Bolton 1980](https://doi.org/10.1175/1520-0493(1980)108%3C1046:TCOEPT%3E2.0.CO;2)
 """
 
 import numpy as np

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/saturation_vapour_pressure/lowe1977.py

@@ -1,6 +1,6 @@
 """
 polynomial fits from
-[Lowe et al. 1977](https://doi.org/10.1175/1520-0450(1977)016<0100:AAPFTC>2.0.CO;2)
+[Lowe et al. 1977](https://doi.org/10.1175/1520-0450(1977)016%3C0100:AAPFTC%3E2.0.CO;2)
 """
 
 

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/saturation_vapour_pressure/wexler_1976.py

@@ -1,5 +1,5 @@
 """
-[Wexler 1976](https://nvlpubs.nist.gov/nistpubs/jres/80A/jresv80An5-6p775_A1b.pdf)
+[Wexler 1976](https://doi.org/10.6028/jres.080A.071)
 """
 
 import numpy as np

{pysdm-2.93 → pysdm-2.95}/PySDM/physics/ventilation/pruppacher_rasmussen_1979.py

@@ -1,7 +1,7 @@
 """
 ventilation coefficient as a function of dimensionless Reynolds (Re) and Schmidt (Sc)
 numbers for liquid drops following
-[Pruppacher & Rasmussen (1979)](https://doi.org/10.1175/1520-0469(1979)036<1255:AWTIOT>2.0.CO;2)
+[Pruppacher & Rasmussen (1979)](https://doi.org/10.1175/1520-0469(1979)036%3C1255:AWTIOT%3E2.0.CO;2)
 NB: this parameterization is only experimentally validated for Re < 2600
 but is hypothesized to be valid for spheres with Re < 8 × 10⁴
 based on theory (Pruppacher & Rasmussen, 1979).

{pysdm-2.93 → pysdm-2.95}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.93
+Version: 2.95
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors

{pysdm-2.93 → pysdm-2.95}/PySDM.egg-info/SOURCES.txt

@@ -412,6 +412,8 @@ PySDM/products/size_spectral/size_standard_deviation.py
 PySDM/products/size_spectral/total_particle_concentration.py
 PySDM/products/size_spectral/total_particle_specific_concentration.py
 PySDM/products/size_spectral/water_mixing_ratio.py
+docs/bibliography.json
+docs/generate_html.py
 docs/logos/pysdm_logo.png
 docs/logos/pysdm_logo.svg
 docs/markdown/pysdm_landing.md
@@ -455,7 +457,6 @@ examples/PySDM_examples/Arabas_et_al_2015/__init__.py
 examples/PySDM_examples/Arabas_et_al_2015/example.py
 examples/PySDM_examples/Arabas_et_al_2015/example_benchmark.py
 examples/PySDM_examples/Arabas_et_al_2015/gui.ipynb
-examples/PySDM_examples/Arabas_et_al_2015/paraview_hello_world.ipynb
 examples/PySDM_examples/Arabas_et_al_2015/settings.py
 examples/PySDM_examples/Arabas_et_al_2015/spin_up.py
 examples/PySDM_examples/Arabas_et_al_2023/__init__.py
@@ -615,7 +616,9 @@ examples/PySDM_examples/Yang_et_al_2018/__init__.py
 examples/PySDM_examples/Yang_et_al_2018/fig_2.ipynb
 examples/PySDM_examples/Yang_et_al_2018/settings.py
 examples/PySDM_examples/Yang_et_al_2018/simulation.py
+examples/PySDM_examples/_HOWTOs/__init__.py
 examples/PySDM_examples/_HOWTOs/dimensional_analysis.ipynb
+examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb
 examples/PySDM_examples/deJong_Azimi/__init__.py
 examples/PySDM_examples/deJong_Azimi/box.ipynb
 examples/PySDM_examples/deJong_Azimi/cloudy_data.py