From 11741b0e6122b98eafdf28115df7d2f1a0de7b7c Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Fri, 11 Aug 2023 13:00:27 +0200 Subject: [PATCH 1/7] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fd30ef9f..464a8bea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ rtd = [ "Ipython", "ipykernel", "pydata-sphinx-theme", - "sphinx>=3.1, <6.0", + "sphinx>=5", "sphinxcontrib-bibtex", "requests", "numpydoc", From 66db3c233840460383088719b299e8fc11ceba1f Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Fri, 11 Aug 2023 13:19:12 +0200 Subject: [PATCH 2/7] try using myst --- doc/conf.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 4500c4e4..12cdcb42 100755 --- a/doc/conf.py +++ b/doc/conf.py @@ -35,8 +35,8 @@ "sphinx.ext.ifconfig", "sphinx.ext.viewcode", "IPython.sphinxext.ipython_console_highlighting", # lowercase didn't work - "nbsphinx", - "numpydoc", + # "nbsphinx", + "myst_nb", "sphinxcontrib.bibtex", "sphinx_design", "sphinx.ext.autosectionlabel", @@ -174,3 +174,8 @@ nbsphinx_allow_errors = True # Allow errors in notebooks, to see the error online nbsphinx_execute = "auto" + +# -- myst_nb options ------------------------------------------------------------------ + +nb_execution_mode = "auto" +nb_execution_allow_errors = True From 32a9773c9c178ea228bd981cbc64eda6ff078c3e Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Fri, 11 Aug 2023 13:27:28 +0200 Subject: [PATCH 3/7] Update pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 464a8bea..61a64840 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,6 +71,7 @@ rtd = [ "requests", "numpydoc", "sphinx-design", + "myst_nb", ] dev = ["tox", "pastas[formatting,linting,ci,rtd]"] numbascipy = ["numba-scipy >= 0.3.1"] From 9f9117e77fe243f965a1d78079ac353c28b52edb Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Fri, 11 Aug 2023 14:43:19 +0200 Subject: [PATCH 4/7] remove nbsphinx dependency --- doc/conf.py | 11 +++-------- pyproject.toml | 3 +-- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 12cdcb42..9bf90ea6 100755 --- a/doc/conf.py +++ b/doc/conf.py @@ -35,7 +35,7 @@ "sphinx.ext.ifconfig", "sphinx.ext.viewcode", "IPython.sphinxext.ipython_console_highlighting", # lowercase didn't work - # "nbsphinx", + "numpydoc", "myst_nb", "sphinxcontrib.bibtex", "sphinx_design", @@ -52,7 +52,7 @@ # General information about the project. project = "Pastas" -copyright = "{}, R.A. Collenteur, M. Bakker, R. Calje, F. Schaars".format(year) +copyright = "{}, The Pastas Team".format(year) author = "R.A. Collenteur, M. Bakker, R. Calje, F. Schaars" # The version. @@ -170,12 +170,7 @@ "matplotlib": ("https://matplotlib.org/stable", None), } -# -- nbsphinx options---------- ------------------------------------------------------- - -nbsphinx_allow_errors = True # Allow errors in notebooks, to see the error online -nbsphinx_execute = "auto" - # -- myst_nb options ------------------------------------------------------------------ +nb_execution_allow_errors = True # Allow errors in notebooks, to see the error online nb_execution_mode = "auto" -nb_execution_allow_errors = True diff --git a/pyproject.toml b/pyproject.toml index 61a64840..93873e35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,11 +62,10 @@ ci = [ ] rtd = [ "pastas[solvers]", - "nbsphinx", "Ipython", "ipykernel", "pydata-sphinx-theme", - "sphinx>=5", + "sphinx>=3.1, <6.0", "sphinxcontrib-bibtex", "requests", "numpydoc", From 902b7321461dc074081aa99073f6834cb866dc4b Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Wed, 16 Aug 2023 16:10:33 +0200 Subject: [PATCH 5/7] Update index.rst --- doc/examples/index.rst | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/doc/examples/index.rst b/doc/examples/index.rst index 824c2c24..e4d153bf 100644 --- a/doc/examples/index.rst +++ b/doc/examples/index.rst @@ -45,11 +45,11 @@ Basics `Modeling with different timesteps`_ -.. _Preprocessing user-provided time series: prepare_timeseries.ipynb -.. _A basic model: basic_model.ipynb -.. _Fixating parameters while fitting: fix_parameters.ipynb -.. _Calibration: calibration_options.ipynb -.. _Modeling with different timesteps: modeling_timestep.ipynb +.. _Preprocessing user-provided time series: prepare_timeseries +.. _A basic model: basic_model +.. _Fixating parameters while fitting: fix_parameters +.. _Calibration: calibration_options +.. _Modeling with different timesteps: modeling_timestep Stressmodels ------------ @@ -64,11 +64,11 @@ Stressmodels `Changing response functions`_ -.. _Adding surface water levels: adding_rivers.ipynb -.. _Adding pumping wells: adding_wells.ipynb -.. _Adding multiple wells: multiple_wells.ipynb -.. _Adding trends: adding_trends.ipynb -.. _Changing response functions: changing_responses.ipynb +.. _Adding surface water levels: adding_rivers +.. _Adding pumping wells: adding_wells +.. _Adding multiple wells: multiple_wells +.. _Adding trends: adding_trends +.. _Changing response functions: changing_responses Non-linear (Recharge) Models ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -81,10 +81,10 @@ Non-linear (Recharge) Models `Modeling snow`_ -.. _Threshold non-linearities: threshold_non_linear.ipynb -.. _Non-linear recharge models: non_linear_recharge.ipynb -.. _Estimating recharge: recharge_estimation.ipynb -.. _Modeling snow: snowmodel.ipynb +.. _Threshold non-linearities: threshold_non_linear +.. _Non-linear recharge models: non_linear_recharge +.. _Estimating recharge: recharge_estimation +.. _Modeling snow: snowmodel Model Evaluation @@ -100,11 +100,11 @@ Model Evaluation `MCMC uncertainty`_ -.. _Comparing models visually: comparing_models.ipynb -.. _Diagnostic checking: diagnostic_checking.ipynb -.. _`Reducing autocorrelation`: timestep_analysis.ipynb -.. _Uncertainty quantification: uncertainty.ipynb -.. _MCMC uncertainty: uncertainty_emcee.ipynb +.. _Comparing models visually: comparing_models +.. _Diagnostic checking: diagnostic_checking +.. _`Reducing autocorrelation`: timestep_analysis +.. _Uncertainty quantification: uncertainty +.. _MCMC uncertainty: uncertainty_emcee Applications @@ -114,8 +114,8 @@ Applications `Groundwater signatures`_ -.. _Standardized Groundwater Index: standardized_groundwater_index.ipynb -.. _Groundwater signatures: signatures.ipynb +.. _Standardized Groundwater Index: standardized_groundwater_index +.. _Groundwater signatures: signatures STOWA Manual (Dutch only) From 5db4ab5fc309aef5d2cc8e22765e32f6567ae0ed Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Wed, 16 Aug 2023 16:53:27 +0200 Subject: [PATCH 6/7] Update index.rst --- doc/examples/index.rst | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/doc/examples/index.rst b/doc/examples/index.rst index e4d153bf..b979fbb2 100644 --- a/doc/examples/index.rst +++ b/doc/examples/index.rst @@ -46,10 +46,10 @@ Basics `Modeling with different timesteps`_ .. _Preprocessing user-provided time series: prepare_timeseries -.. _A basic model: basic_model -.. _Fixating parameters while fitting: fix_parameters -.. _Calibration: calibration_options -.. _Modeling with different timesteps: modeling_timestep +.. _A basic model: basic_model.html +.. _Fixating parameters while fitting: fix_parameters.html +.. _Calibration: calibration_options.html +.. _Modeling with different timesteps: modeling_timestep.html Stressmodels ------------ @@ -64,11 +64,11 @@ Stressmodels `Changing response functions`_ -.. _Adding surface water levels: adding_rivers -.. _Adding pumping wells: adding_wells -.. _Adding multiple wells: multiple_wells -.. _Adding trends: adding_trends -.. _Changing response functions: changing_responses +.. _Adding surface water levels: adding_rivers.html +.. _Adding pumping wells: adding_wells.html +.. _Adding multiple wells: multiple_wells.html +.. _Adding trends: adding_trends.html +.. _Changing response functions: changing_responses.html Non-linear (Recharge) Models ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -81,10 +81,10 @@ Non-linear (Recharge) Models `Modeling snow`_ -.. _Threshold non-linearities: threshold_non_linear -.. _Non-linear recharge models: non_linear_recharge -.. _Estimating recharge: recharge_estimation -.. _Modeling snow: snowmodel +.. _Threshold non-linearities: threshold_non_linear.html +.. _Non-linear recharge models: non_linear_recharge.html +.. _Estimating recharge: recharge_estimation.html +.. _Modeling snow: snowmodel.html Model Evaluation @@ -100,11 +100,11 @@ Model Evaluation `MCMC uncertainty`_ -.. _Comparing models visually: comparing_models -.. _Diagnostic checking: diagnostic_checking -.. _`Reducing autocorrelation`: timestep_analysis -.. _Uncertainty quantification: uncertainty -.. _MCMC uncertainty: uncertainty_emcee +.. _Comparing models visually: comparing_models.html +.. _Diagnostic checking: diagnostic_checking.html +.. _`Reducing autocorrelation`: timestep_analysis.html +.. _Uncertainty quantification: uncertainty.html +.. _MCMC uncertainty: uncertainty_emcee.html Applications @@ -114,8 +114,8 @@ Applications `Groundwater signatures`_ -.. _Standardized Groundwater Index: standardized_groundwater_index -.. _Groundwater signatures: signatures +.. _Standardized Groundwater Index: standardized_groundwater_index.html +.. _Groundwater signatures: signatures.html STOWA Manual (Dutch only) From ad0bf378fd029a99a6c8fdc4f457381e6ac64123 Mon Sep 17 00:00:00 2001 From: Raoul Collenteur Date: Wed, 16 Aug 2023 19:36:07 +0200 Subject: [PATCH 7/7] Update index.rst --- doc/examples/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/examples/index.rst b/doc/examples/index.rst index b979fbb2..46308904 100644 --- a/doc/examples/index.rst +++ b/doc/examples/index.rst @@ -45,7 +45,7 @@ Basics `Modeling with different timesteps`_ -.. _Preprocessing user-provided time series: prepare_timeseries +.. _Preprocessing user-provided time series: prepare_timeseries.html .. _A basic model: basic_model.html .. _Fixating parameters while fitting: fix_parameters.html .. _Calibration: calibration_options.html