From 568eb4534e5c8f616e05a40c147b591798c7fb38 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 21:54:13 +0200 Subject: [PATCH 1/9] Add em space --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index b51d08c..a931f43 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -49,7 +49,7 @@ Supported by Development of BikeNetKit/GrowBikeNet was supported by the Innovation Fund Denmark and the EU HORIZON grant JUST STREETS. -|Innovation Fund Denmark| |European Union| |JUST STREETS| +|Innovation Fund Denmark| |European Union| |JUST STREETS| .. |Innovation Fund Denmark| image:: _static/logo_innovationfund.png :target: https://innovationsfonden.dk/en From e1069e125af16b56eb0e3fb84399b12028804315 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:01:49 +0200 Subject: [PATCH 2/9] Update install info to work in current situation --- docs/source/installation.rst | 100 ++++++++++++++--------------------- 1 file changed, 41 insertions(+), 59 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index d252fd3..c3eb35d 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -21,32 +21,31 @@ Set up environment The main step is to set up a virtual environment ``gbnenv`` in which to install the package, and then to use or run the environment. -With Pixi -''''''''' +With conda/pip +'''''''''''''' -Installation with `Pixi `__ is -fastest and most stable: - -:: +Installation with `conda `__ (or the faster `mamba `__). - pixi init gbnenv - pixi add --pypi growbikenet +The conda-forge installation is not yet working. -At this point you can run growbikenet in the environment, for example as -such: +Therefore, you need to `clone the +repository `__ +and create the environment via the +``environment.yml`` file: :: - pixi run python examples/mwe.py + conda env create --file environment.yml + conda activate gbnenv + pip install growbikenet -.. - | [NOTE] - | The first time you run code with Pixi, it might take a minute - longer, as Pixi resolves the environment’s dependencies only at - this point. +With Pixi +''''''''' + +Installation with `Pixi `__. -*Alternatively*, or if you run into issues, `clone this +First, `clone this repository `__ and create the environment via the ``environment.yml`` file: @@ -55,35 +54,18 @@ and create the environment via the pixi init --import environment.yml -With mamba/conda/pip -'''''''''''''''''''' - -Alternatively to Pixi, use -`mamba `__ or -`conda `__. - - -.. - - | [IMPORTANT] - | As of 2026-05-04, the conda-forge installation is not yet working. - We will remove this note once it works. +At this point you can run growbikenet in the environment, for example as +such: :: - mamba create -n gbnenv -c conda-forge growbikenet - mamba activate gbnenv - -*Alternatively*, or if you run into issues, `clone the -repository `__ -and create the environment via the -``environment.yml`` file: + pixi run python examples/mwe.py -:: +.. - mamba env create --file environment.yml - mamba activate gbnenv - pip install growbikenet + | The first time you run code with Pixi, it might take a minute + longer, as Pixi resolves the environment’s dependencies only at + this point. Run growbikenet in Jupyter lab @@ -93,29 +75,16 @@ After having set up the environment above, if you wish to run growbikenet via `JupyterLab `__, follow the instructions below. -With Pixi -^^^^^^^^^ +With conda +^^^^^^^^^^ -Running growbikenet in Jupter lab with -`Pixi `__ is straightforward: +Using `conda `__ (or the faster `mamba `__), run: :: - pixi run jupyter lab - -An instance of Jupyter lab is automatically going to open in your -browser after the environment is built. - -With mamba/conda -^^^^^^^^^^^^^^^^ - -Using mamba/conda, run: - -:: - - mamba activate gbnenv + conda activate gbnenv ipython kernel install --user --name=gbnenv - mamba deactivate + conda deactivate jupyter lab Once Jupyter lab opens, switch the kernel (Kernel > Change Kernel > @@ -136,6 +105,19 @@ Once Jupyter lab opens, switch the kernel (Kernel > Change Kernel > gbnenv) +With Pixi +^^^^^^^^^ + +Running growbikenet in Jupter lab with +`Pixi `__ is straightforward: + +:: + + pixi run jupyter lab + +An instance of Jupyter lab is automatically going to open in your +browser after the environment is built. + Development installation ~~~~~~~~~~~~~~~~~~~~~~~~ From 7c385d966965ade79b158dc48866eaeb17ff8d72 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:05:18 +0200 Subject: [PATCH 3/9] Make spaces consistent with readme --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index a931f43..3fe255e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -49,7 +49,7 @@ Supported by Development of BikeNetKit/GrowBikeNet was supported by the Innovation Fund Denmark and the EU HORIZON grant JUST STREETS. -|Innovation Fund Denmark| |European Union| |JUST STREETS| +|Innovation Fund Denmark|  |European Union| |JUST STREETS| .. |Innovation Fund Denmark| image:: _static/logo_innovationfund.png :target: https://innovationsfonden.dk/en From c10d80c5e52436fc0eb126447c7ff84e64c1c4bd Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:18:38 +0200 Subject: [PATCH 4/9] Polish install instructions --- README.md | 2 +- docs/source/getting_started.rst | 2 +- docs/source/installation.rst | 7 +++---- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index f4c8839..97bef3d 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The software downloads and pre-processes data from OpenStreetMap, prepares seed ### The easy way -The currently best way to install GrowBikeNet is using pip: +The currently default way to install GrowBikeNet is using pip: ``` pip install growbikenet diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index ed0d6c9..8d0a774 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -8,7 +8,7 @@ Get Started in 4 Steps 2. Read the :ref:`introducing-growbikenet` section below. -3. Run the :doc:`mwe`. +3. To check that the installation worked, run ``python examples/mwe.py`` or the Jupyter :doc:`mwe`. 4. Consult the :doc:`reference_user` for complete details on using the package. diff --git a/docs/source/installation.rst b/docs/source/installation.rst index c3eb35d..1acedae 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -5,12 +5,13 @@ Installation The easy way ~~~~~~~~~~~~ -The currently best way to install GrowBikeNet is using pip: +The currently default way to install GrowBikeNet is using pip: :: pip install growbikenet +If this does not work, follow the instructions below. Advanced installations ~~~~~~~~~~~~~~~~~~~~~~ @@ -26,9 +27,7 @@ With conda/pip Installation with `conda `__ (or the faster `mamba `__). -The conda-forge installation is not yet working. - -Therefore, you need to `clone the +The conda-forge installation is not yet working. Therefore, you need to `clone the repository `__ and create the environment via the ``environment.yml`` file: From a6394dfcbd7f59974bb19d0a1078510b730ae207 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:21:16 +0200 Subject: [PATCH 5/9] Change bibtex style to plain --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 5622d9c..f57130d 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -52,6 +52,7 @@ # path to bib file with references bibtex_bibfiles = ["_static/references.bib"] bibtex_reference_style = "author_year" +bibtex_default_style = 'plain' # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output From de9deac2ce665212a710dc58c521e1b651043af1 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:22:20 +0200 Subject: [PATCH 6/9] Make spaces consistent with readme --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 3fe255e..d4e2e01 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -49,7 +49,7 @@ Supported by Development of BikeNetKit/GrowBikeNet was supported by the Innovation Fund Denmark and the EU HORIZON grant JUST STREETS. -|Innovation Fund Denmark|  |European Union| |JUST STREETS| +|Innovation Fund Denmark|    |European Union|   |JUST STREETS| .. |Innovation Fund Denmark| image:: _static/logo_innovationfund.png :target: https://innovationsfonden.dk/en From a151d11694b2ae523a30fe5687b2e6188fb12edc Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:24:46 +0200 Subject: [PATCH 7/9] Fix typo --- README.md | 2 +- docs/source/index.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 97bef3d..d6ecf40 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ The Python package `growbikenet` grows an urban bicycle network from scratch or from an existing bicycle network. -The software downloads and pre-processes data from OpenStreetMap, prepares seed points to connect, runs simulations, saves the results, create plots and videos. The source code builds on [the code from the research paper](https://github.com/mszell/bikenwgrowth) _Growing Urban Bicycle Networks_ and on [the code from the research paper](https://github.com/pietrofolco/Data-driven_bicycle_network_planning_for_demand_and_safety) _Data-driven micromobility network planning for demand and safety_. +The software downloads and pre-processes data from OpenStreetMap, prepares seed points to connect, runs simulations, saves the results, creates plots and videos. The source code builds on [the code from the research paper](https://github.com/mszell/bikenwgrowth) _Growing Urban Bicycle Networks_ and on [the code from the research paper](https://github.com/pietrofolco/Data-driven_bicycle_network_planning_for_demand_and_safety) _Data-driven micromobility network planning for demand and safety_. **Publication** (primary): [https://doi.org/10.1038/s41598-022-10783-y](https://doi.org/10.1038/s41598-022-10783-y) **Publication** (secondary): [https://doi.org/10.1177/23998083221135611](https://doi.org/10.1177/23998083221135611) diff --git a/docs/source/index.rst b/docs/source/index.rst index d4e2e01..5cc8b46 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -10,7 +10,7 @@ The Python package ``growbikenet`` grows an urban bicycle network from scratch o The software downloads and pre-processes data from OpenStreetMap, prepares seed points to connect, runs simulations, saves the results, -create plots and videos. The source code builds on `the code from the +creates plots and videos. The source code builds on `the code from the research paper `__ *Growing Urban Bicycle Networks* and on `the code from the research paper `__ From d8acffd6ab2e53165255a9b98e20ee037e0bf474 Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:34:50 +0200 Subject: [PATCH 8/9] Simplify install docs hierarchy --- docs/source/installation.rst | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 1acedae..c051d12 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -16,14 +16,11 @@ If this does not work, follow the instructions below. Advanced installations ~~~~~~~~~~~~~~~~~~~~~~ -Set up environment -^^^^^^^^^^^^^^^^^^ - The main step is to set up a virtual environment ``gbnenv`` in which to install the package, and then to use or run the environment. With conda/pip -'''''''''''''' +^^^^^^^^^^^^^^ Installation with `conda `__ (or the faster `mamba `__). @@ -40,7 +37,7 @@ and create the environment via the With Pixi -''''''''' +^^^^^^^^^ Installation with `Pixi `__. From 8a0b5a6dd9f7f126436c3a7a37c949a4eebb765f Mon Sep 17 00:00:00 2001 From: Michael Szell Date: Mon, 25 May 2026 22:39:37 +0200 Subject: [PATCH 9/9] Polish install instructions --- docs/source/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index c051d12..ec547bd 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -17,7 +17,7 @@ Advanced installations ~~~~~~~~~~~~~~~~~~~~~~ The main step is to set up a virtual environment ``gbnenv`` in which to -install the package, and then to use or run the environment. +install the package, and then to use or run the environment. Use either of the methods below. With conda/pip ^^^^^^^^^^^^^^ @@ -69,7 +69,7 @@ Run growbikenet in Jupyter lab After having set up the environment above, if you wish to run growbikenet via `JupyterLab `__, -follow the instructions below. +follow the corresponding instructions below. With conda ^^^^^^^^^^