Bibliography in documentation (data in .json file, scripts checking c…

…onsistency with DOI mentions in the codebase) (#1483) Co-authored-by: Sylwester Arabas <[email protected]>
open-atmos · Jan 2, 2025 · a16f63f · a16f63f
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diff --git a/.github/workflows/docs.py b/.github/workflows/docs.py
diff --git a/.github/workflows/pdoc.yml b/.github/workflows/pdoc.yml
@@ -27,11 +27,11 @@ jobs:
         with:
           python-version: "3.12"
       - run: |
-          pip install pdoc nbformat
+          pip install pdoc nbformat gitpython
           pip install -e .
           pip install -e examples
 
-          python -We .github/workflows/docs.py . .
+          python -We docs/generate_html.py . .
         
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
         uses: JamesIves/[email protected]

diff --git a/PySDM/backends/impl_numba/methods/chemistry_methods.py b/PySDM/backends/impl_numba/methods/chemistry_methods.py
@@ -234,8 +234,8 @@ def oxidation_body(  # pylint: disable=too-many-locals
             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 = (
                 (

diff --git a/PySDM/dynamics/collisions/breakup_fragmentations/feingold1988.py b/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

diff --git a/PySDM/dynamics/collisions/breakup_fragmentations/lowlist82.py b/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

diff --git a/PySDM/physics/constants_defaults.py b/PySDM/physics/constants_defaults.py
@@ -193,7 +193,7 @@
 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_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_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_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 @@
 """ 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_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_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

diff --git a/PySDM/physics/isotope_equilibrium_fractionation_factors/van_hook_1968.py b/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

diff --git a/PySDM/physics/isotope_ratio_evolution/merlivat_and_jouzel_1979.py b/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))
 """
 
 

diff --git a/PySDM/physics/saturation_vapour_pressure/bolton_1980.py b/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

diff --git a/PySDM/physics/saturation_vapour_pressure/lowe1977.py b/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)
 """
 
 

diff --git a/PySDM/physics/saturation_vapour_pressure/wexler_1976.py b/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

diff --git a/PySDM/physics/ventilation/pruppacher_rasmussen_1979.py b/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).