From 01318713d8ea177d721bf8f2e2eb125a88211bf5 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Sun, 11 May 2025 17:23:37 -0700
Subject: [PATCH 01/11] pull out environment directions from contributor
 install guide

---
 content/how-tos/envs.md | 123 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 123 insertions(+)
 create mode 100644 content/how-tos/envs.md

diff --git a/content/how-tos/envs.md b/content/how-tos/envs.md
new file mode 100644
index 0000000..3d3e50c
--- /dev/null
+++ b/content/how-tos/envs.md
@@ -0,0 +1,123 @@
+---
+title: How to set up a virtual environment
+---
+
+In this guide we summarize some key commands to set up a virtual environment
+with different tools in the scientific python ecosystem. 
+A virtual environment is a workspace into which you can install Python
+libraries, separate from what is being used by your operating system.
+
+The environment managers that are covered in this how-to guide include:
+- venv
+- conda
+- mamba
+- uv
+- pixi
+
+In each of these examples we'll create a new virtual environment related to our project called `science` 
+(you can use whichever name you prefer!). We'll activate the environment, install some dependencies, and see 
+an example of installing dependencies from a file. 
+
+### Set up a virtual environment with venv
+
+With venv we'll have our virtual environment associated with our project folder called `science`. 
+
+```
+python -m venv science
+```
+
+Start using it by activating it as follows:
+
+```
+source science/bin/activate
+```
+
+You are now ready to install Scientific Python packages using `pip`! For example:
+
+```
+pip install ipython numpy scipy
+```
+
+Often you'll interact with projects that have a specific list of dependencies (for development 
+environments, testing environments, or the project itself). You can install the list of dependencies
+with pip in your venv using: 
+
+```
+pip install -r requirements.txt
+```
+
+Remember to re-activate your environment every time you open a new terminal, using:
+
+```
+source science/bin/activate
+```
+
+### Set up a virtual environment using conda 
+
+With conda, we can create a new environment named science (-n is the same as passing --name):
+
+```
+conda create -n science
+```
+
+Start using your environment by activating it: 
+
+```
+conda activate science
+```
+
+You are now ready to install Scientific Python packages using `conda`!
+For example:
+
+```
+conda install ipython numpy scipy
+```
+
+Often you'll interact with projects that have a specific list of dependencies (for development 
+environments, testing environments, or the project itself). You can install the list of dependencies
+with conda in your environment using: 
+
+```
+conda install --file requirements.txt
+```
+
+Remember to re-activate your environment every time you open a new terminal:
+
+```
+conda activate science
+```
+
+### Set up a virtual environment using mamba 
+
+With mamba, like conda, we can create a new environment named science (-n is the same as passing --name):
+
+```
+mamba create -n science
+```
+
+Start using your environment by activating it: 
+
+```
+mamba activate science
+```
+
+You are now ready to install Scientific Python packages using `mamba`!
+For example:
+
+```
+mamba install ipython numpy scipy
+```
+
+Often you'll interact with projects that have a specific list of dependencies (for development 
+environments, testing environments, or the project itself). You can install the list of dependencies
+with mamba in your environment using: 
+
+```
+mamba install --file requirements.txt
+```
+
+Remember to re-activate your environment every time you open a new terminal:
+
+```
+mamba activate science
+```

From e6dc8c9f8ef0e83f4ef9eb39191192f9a68471e8 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Mon, 12 May 2025 14:30:44 -0700
Subject: [PATCH 02/11] add in pixi and uv commands

---
 ...{envs.md => how-to-create-environments.md} | 100 ++++++++++++++++--
 1 file changed, 89 insertions(+), 11 deletions(-)
 rename content/how-tos/{envs.md => how-to-create-environments.md} (52%)

diff --git a/content/how-tos/envs.md b/content/how-tos/how-to-create-environments.md
similarity index 52%
rename from content/how-tos/envs.md
rename to content/how-tos/how-to-create-environments.md
index 3d3e50c..ff10707 100644
--- a/content/how-tos/envs.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -43,7 +43,7 @@ environments, testing environments, or the project itself). You can install the
 with pip in your venv using: 
 
 ```
-pip install -r requirements.txt
+pip install -r <path/to/requirements.txt>
 ```
 
 Remember to re-activate your environment every time you open a new terminal, using:
@@ -52,7 +52,7 @@ Remember to re-activate your environment every time you open a new terminal, usi
 source science/bin/activate
 ```
 
-### Set up a virtual environment using conda 
+### Set up an environment using conda 
 
 With conda, we can create a new environment named science (-n is the same as passing --name):
 
@@ -73,12 +73,12 @@ For example:
 conda install ipython numpy scipy
 ```
 
-Often you'll interact with projects that have a specific list of dependencies (for development 
-environments, testing environments, or the project itself). You can install the list of dependencies
-with conda in your environment using: 
+Some projects distribute environment files with listed dependencies with an `environment.yml` file. 
+The first line of this file sets the environment's name. To
+create an environment and install the dependencies with this file, use: 
 
 ```
-conda install --file requirements.txt
+conda env create -f <path/to/environment.yml>
 ```
 
 Remember to re-activate your environment every time you open a new terminal:
@@ -87,7 +87,7 @@ Remember to re-activate your environment every time you open a new terminal:
 conda activate science
 ```
 
-### Set up a virtual environment using mamba 
+### Set up an environment using mamba 
 
 With mamba, like conda, we can create a new environment named science (-n is the same as passing --name):
 
@@ -108,12 +108,10 @@ For example:
 mamba install ipython numpy scipy
 ```
 
-Often you'll interact with projects that have a specific list of dependencies (for development 
-environments, testing environments, or the project itself). You can install the list of dependencies
-with mamba in your environment using: 
+To install a specific environment from a `.yml` file, use: 
 
 ```
-mamba install --file requirements.txt
+mamba create -f </path/to/environment.yml>
 ```
 
 Remember to re-activate your environment every time you open a new terminal:
@@ -121,3 +119,83 @@ Remember to re-activate your environment every time you open a new terminal:
 ```
 mamba activate science
 ```
+
+### Set up a virtual environment using uv 
+
+To create a new environment using uv in our project folder called `science`:  
+
+```
+uv venv
+```
+
+Start using your environment by activating it: 
+
+```
+source .venv/bin/activate
+```
+
+You are now ready to install Scientific Python packages using `uv`!
+For example:
+
+```
+uv pip install ipython numpy scipy
+```
+
+To install dependencies from a requirements file, use: 
+
+```
+uv pip install -f </path/to/requirements.txt>
+```
+
+Remember to re-activate your environment time you open a new terminal:
+
+```
+source <path/to/science/>.venv/bin/activate
+```
+
+You can find more information on using uv for environments 
+[here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
+
+### Set up a virtual environment using pixi 
+
+To initialize a new project with pixi in our project called `science`, execute:   
+
+```
+pixi init 
+```
+
+You are now ready to install Scientific Python packages as dependencies in this project!
+From the science directory, execute:
+
+```
+pixi add ipython numpy scipy
+```
+
+To install dependencies from a file like `environment.yml`, use: 
+
+```
+pixi init --import <path/to/environment.yml>
+```
+
+Remember to re-activate your environment when you re-open a terminal. Navigate to 
+the science folder, and execute:
+
+```
+pixi shell 
+```
+
+A pixi project may have multiple environments defined in the `pixi.toml` file. To 
+load a specific environment: 
+
+```
+pixi shell --environment=<envname> 
+```
+
+You can find more information on using pixi  
+[here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
+
+
+
+
+
+

From f801bbb751e8eb44ff66b18939ffd769dda0832a Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Mon, 12 May 2025 14:53:06 -0700
Subject: [PATCH 03/11] add links to docs for each tool

---
 content/how-tos/how-to-create-environments.md | 30 +++++++++++++------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index ff10707..7c08c61 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -1,10 +1,10 @@
 ---
-title: How to set up a virtual environment
+title: How to set up an environment
 ---
 
-In this guide we summarize some key commands to set up a virtual environment
-with different tools in the scientific python ecosystem. 
-A virtual environment is a workspace into which you can install Python
+In this guide we summarize some key commands to set up an environment
+with different tools that you might encounter in the scientific python 
+ecosystem. An environment is a workspace into which you can install Python
 libraries, separate from what is being used by your operating system.
 
 The environment managers that are covered in this how-to guide include:
@@ -14,13 +14,16 @@ The environment managers that are covered in this how-to guide include:
 - uv
 - pixi
 
-In each of these examples we'll create a new virtual environment related to our project called `science` 
-(you can use whichever name you prefer!). We'll activate the environment, install some dependencies, and see 
-an example of installing dependencies from a file. 
+In each of these examples we'll create a new virtual environment related to our 
+project called `science` (you can use whichever name you prefer!). We'll activate 
+the environment, install some dependencies, and see 
+an example of installing dependencies from an existing file. You may encounter 
+files like `requirements.txt`, `environment.yml` or `pyproject.toml` that specify 
+needed dependencies for a project.  
 
 ### Set up a virtual environment with venv
 
-With venv we'll have our virtual environment associated with our project folder called `science`. 
+With venv to create  environment associated with a project folder called `science`. 
 
 ```
 python -m venv science
@@ -52,6 +55,9 @@ Remember to re-activate your environment every time you open a new terminal, usi
 source science/bin/activate
 ```
 
+You can find more information on using venv for packaging 
+[here](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/).
+
 ### Set up an environment using conda 
 
 With conda, we can create a new environment named science (-n is the same as passing --name):
@@ -87,6 +93,9 @@ Remember to re-activate your environment every time you open a new terminal:
 conda activate science
 ```
 
+You can find more information on using conda for environments  
+[here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
+
 ### Set up an environment using mamba 
 
 With mamba, like conda, we can create a new environment named science (-n is the same as passing --name):
@@ -120,6 +129,9 @@ Remember to re-activate your environment every time you open a new terminal:
 mamba activate science
 ```
 
+You can find more information on using mamba in the   
+[mamba user guide](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html).
+
 ### Set up a virtual environment using uv 
 
 To create a new environment using uv in our project folder called `science`:  
@@ -192,7 +204,7 @@ pixi shell --environment=<envname>
 ```
 
 You can find more information on using pixi  
-[here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
+[here](https://prefix.dev/docs/pixi/basic_usage).
 
 
 

From 3052c7d7bdcd98b497b216649ce3ae765adba000 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Mon, 12 May 2025 15:02:41 -0700
Subject: [PATCH 04/11] add shell highlighting for environment commands

---
 content/how-tos/how-to-create-environments.md | 56 ++++++++++---------
 1 file changed, 30 insertions(+), 26 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index 7c08c61..cdb6a9b 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -25,19 +25,19 @@ needed dependencies for a project.
 
 With venv to create  environment associated with a project folder called `science`. 
 
-```
+```shell
 python -m venv science
 ```
 
 Start using it by activating it as follows:
 
-```
+```shell
 source science/bin/activate
 ```
 
 You are now ready to install Scientific Python packages using `pip`! For example:
 
-```
+```shell
 pip install ipython numpy scipy
 ```
 
@@ -45,13 +45,13 @@ Often you'll interact with projects that have a specific list of dependencies (f
 environments, testing environments, or the project itself). You can install the list of dependencies
 with pip in your venv using: 
 
-```
+```shell
 pip install -r <path/to/requirements.txt>
 ```
 
 Remember to re-activate your environment every time you open a new terminal, using:
 
-```
+```shell
 source science/bin/activate
 ```
 
@@ -62,20 +62,20 @@ You can find more information on using venv for packaging
 
 With conda, we can create a new environment named science (-n is the same as passing --name):
 
-```
+```shell
 conda create -n science
 ```
 
 Start using your environment by activating it: 
 
-```
+```shell
 conda activate science
 ```
 
 You are now ready to install Scientific Python packages using `conda`!
 For example:
 
-```
+```shell
 conda install ipython numpy scipy
 ```
 
@@ -83,13 +83,13 @@ Some projects distribute environment files with listed dependencies with an `env
 The first line of this file sets the environment's name. To
 create an environment and install the dependencies with this file, use: 
 
-```
+```shell
 conda env create -f <path/to/environment.yml>
 ```
 
 Remember to re-activate your environment every time you open a new terminal:
 
-```
+```shell
 conda activate science
 ```
 
@@ -100,32 +100,32 @@ You can find more information on using conda for environments
 
 With mamba, like conda, we can create a new environment named science (-n is the same as passing --name):
 
-```
+```shell
 mamba create -n science
 ```
 
 Start using your environment by activating it: 
 
-```
+```shell
 mamba activate science
 ```
 
 You are now ready to install Scientific Python packages using `mamba`!
 For example:
 
-```
+```shell
 mamba install ipython numpy scipy
 ```
 
 To install a specific environment from a `.yml` file, use: 
 
-```
+```shell
 mamba create -f </path/to/environment.yml>
 ```
 
 Remember to re-activate your environment every time you open a new terminal:
 
-```
+```shell
 mamba activate science
 ```
 
@@ -134,34 +134,35 @@ You can find more information on using mamba in the
 
 ### Set up a virtual environment using uv 
 
-To create a new environment using uv in our project folder called `science`:  
+To create a new environment using uv in a project folder called `science`, 
+navigate to that folder and execute:  
 
-```
+```shell
 uv venv
 ```
 
 Start using your environment by activating it: 
 
-```
+```shell
 source .venv/bin/activate
 ```
 
 You are now ready to install Scientific Python packages using `uv`!
 For example:
 
-```
+```shell
 uv pip install ipython numpy scipy
 ```
 
 To install dependencies from a requirements file, use: 
 
-```
+```shell
 uv pip install -f </path/to/requirements.txt>
 ```
 
 Remember to re-activate your environment time you open a new terminal:
 
-```
+```shell
 source <path/to/science/>.venv/bin/activate
 ```
 
@@ -172,34 +173,37 @@ You can find more information on using uv for environments
 
 To initialize a new project with pixi in our project called `science`, execute:   
 
-```
+```shell
 pixi init 
 ```
 
 You are now ready to install Scientific Python packages as dependencies in this project!
 From the science directory, execute:
 
-```
+```shell
 pixi add ipython numpy scipy
 ```
 
 To install dependencies from a file like `environment.yml`, use: 
 
-```
+```shell
 pixi init --import <path/to/environment.yml>
 ```
 
 Remember to re-activate your environment when you re-open a terminal. Navigate to 
 the science folder, and execute:
 
-```
+```shell
 pixi shell 
 ```
 
+This will drop you into the default environment for the pixi project, with all 
+dependencies in that environment accessible to you in that shell. 
+
 A pixi project may have multiple environments defined in the `pixi.toml` file. To 
 load a specific environment: 
 
-```
+```shell
 pixi shell --environment=<envname> 
 ```
 

From 3051600b95abb2494816ef77119a63e8f8d3f7c3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 12 May 2025 22:08:22 +0000
Subject: [PATCH 05/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 content/how-tos/how-to-create-environments.md | 83 +++++++++----------
 1 file changed, 39 insertions(+), 44 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index cdb6a9b..dde366f 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -3,27 +3,28 @@ title: How to set up an environment
 ---
 
 In this guide we summarize some key commands to set up an environment
-with different tools that you might encounter in the scientific python 
+with different tools that you might encounter in the scientific python
 ecosystem. An environment is a workspace into which you can install Python
 libraries, separate from what is being used by your operating system.
 
 The environment managers that are covered in this how-to guide include:
+
 - venv
 - conda
 - mamba
 - uv
 - pixi
 
-In each of these examples we'll create a new virtual environment related to our 
-project called `science` (you can use whichever name you prefer!). We'll activate 
-the environment, install some dependencies, and see 
-an example of installing dependencies from an existing file. You may encounter 
-files like `requirements.txt`, `environment.yml` or `pyproject.toml` that specify 
-needed dependencies for a project.  
+In each of these examples we'll create a new virtual environment related to our
+project called `science` (you can use whichever name you prefer!). We'll activate
+the environment, install some dependencies, and see
+an example of installing dependencies from an existing file. You may encounter
+files like `requirements.txt`, `environment.yml` or `pyproject.toml` that specify
+needed dependencies for a project.
 
 ### Set up a virtual environment with venv
 
-With venv to create  environment associated with a project folder called `science`. 
+With venv to create environment associated with a project folder called `science`.
 
 ```shell
 python -m venv science
@@ -41,9 +42,9 @@ You are now ready to install Scientific Python packages using `pip`! For example
 pip install ipython numpy scipy
 ```
 
-Often you'll interact with projects that have a specific list of dependencies (for development 
+Often you'll interact with projects that have a specific list of dependencies (for development
 environments, testing environments, or the project itself). You can install the list of dependencies
-with pip in your venv using: 
+with pip in your venv using:
 
 ```shell
 pip install -r <path/to/requirements.txt>
@@ -55,10 +56,10 @@ Remember to re-activate your environment every time you open a new terminal, usi
 source science/bin/activate
 ```
 
-You can find more information on using venv for packaging 
+You can find more information on using venv for packaging
 [here](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/).
 
-### Set up an environment using conda 
+### Set up an environment using conda
 
 With conda, we can create a new environment named science (-n is the same as passing --name):
 
@@ -66,7 +67,7 @@ With conda, we can create a new environment named science (-n is the same as pas
 conda create -n science
 ```
 
-Start using your environment by activating it: 
+Start using your environment by activating it:
 
 ```shell
 conda activate science
@@ -79,9 +80,9 @@ For example:
 conda install ipython numpy scipy
 ```
 
-Some projects distribute environment files with listed dependencies with an `environment.yml` file. 
+Some projects distribute environment files with listed dependencies with an `environment.yml` file.
 The first line of this file sets the environment's name. To
-create an environment and install the dependencies with this file, use: 
+create an environment and install the dependencies with this file, use:
 
 ```shell
 conda env create -f <path/to/environment.yml>
@@ -93,10 +94,10 @@ Remember to re-activate your environment every time you open a new terminal:
 conda activate science
 ```
 
-You can find more information on using conda for environments  
+You can find more information on using conda for environments
 [here](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
-### Set up an environment using mamba 
+### Set up an environment using mamba
 
 With mamba, like conda, we can create a new environment named science (-n is the same as passing --name):
 
@@ -104,7 +105,7 @@ With mamba, like conda, we can create a new environment named science (-n is the
 mamba create -n science
 ```
 
-Start using your environment by activating it: 
+Start using your environment by activating it:
 
 ```shell
 mamba activate science
@@ -117,7 +118,7 @@ For example:
 mamba install ipython numpy scipy
 ```
 
-To install a specific environment from a `.yml` file, use: 
+To install a specific environment from a `.yml` file, use:
 
 ```shell
 mamba create -f </path/to/environment.yml>
@@ -129,19 +130,19 @@ Remember to re-activate your environment every time you open a new terminal:
 mamba activate science
 ```
 
-You can find more information on using mamba in the   
+You can find more information on using mamba in the
 [mamba user guide](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html).
 
-### Set up a virtual environment using uv 
+### Set up a virtual environment using uv
 
-To create a new environment using uv in a project folder called `science`, 
-navigate to that folder and execute:  
+To create a new environment using uv in a project folder called `science`,
+navigate to that folder and execute:
 
 ```shell
 uv venv
 ```
 
-Start using your environment by activating it: 
+Start using your environment by activating it:
 
 ```shell
 source .venv/bin/activate
@@ -154,7 +155,7 @@ For example:
 uv pip install ipython numpy scipy
 ```
 
-To install dependencies from a requirements file, use: 
+To install dependencies from a requirements file, use:
 
 ```shell
 uv pip install -f </path/to/requirements.txt>
@@ -166,15 +167,15 @@ Remember to re-activate your environment time you open a new terminal:
 source <path/to/science/>.venv/bin/activate
 ```
 
-You can find more information on using uv for environments 
+You can find more information on using uv for environments
 [here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
 
-### Set up a virtual environment using pixi 
+### Set up a virtual environment using pixi
 
-To initialize a new project with pixi in our project called `science`, execute:   
+To initialize a new project with pixi in our project called `science`, execute:
 
 ```shell
-pixi init 
+pixi init
 ```
 
 You are now ready to install Scientific Python packages as dependencies in this project!
@@ -184,34 +185,28 @@ From the science directory, execute:
 pixi add ipython numpy scipy
 ```
 
-To install dependencies from a file like `environment.yml`, use: 
+To install dependencies from a file like `environment.yml`, use:
 
 ```shell
 pixi init --import <path/to/environment.yml>
 ```
 
-Remember to re-activate your environment when you re-open a terminal. Navigate to 
+Remember to re-activate your environment when you re-open a terminal. Navigate to
 the science folder, and execute:
 
 ```shell
-pixi shell 
+pixi shell
 ```
 
-This will drop you into the default environment for the pixi project, with all 
-dependencies in that environment accessible to you in that shell. 
+This will drop you into the default environment for the pixi project, with all
+dependencies in that environment accessible to you in that shell.
 
-A pixi project may have multiple environments defined in the `pixi.toml` file. To 
-load a specific environment: 
+A pixi project may have multiple environments defined in the `pixi.toml` file. To
+load a specific environment:
 
 ```shell
-pixi shell --environment=<envname> 
+pixi shell --environment=<envname>
 ```
 
-You can find more information on using pixi  
+You can find more information on using pixi
 [here](https://prefix.dev/docs/pixi/basic_usage).
-
-
-
-
-
-

From 89c5e179ffcbb56430fec7b726ad692fc0ab6ab0 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Tue, 13 May 2025 15:16:11 -0700
Subject: [PATCH 06/11] Update path for reactivating env for venv

Co-authored-by: Guen Prawiroatmodjo <guenevere.p@gmail.com>
---
 content/how-tos/how-to-create-environments.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index dde366f..3b078bb 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -164,7 +164,8 @@ uv pip install -f </path/to/requirements.txt>
 Remember to re-activate your environment time you open a new terminal:
 
 ```shell
-source <path/to/science/>.venv/bin/activate
+cd <path/to/science/>
+source .venv/bin/activate
 ```
 
 You can find more information on using uv for environments

From 43fde64fa87d383edd223bef947f2947b2cc852f Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Wed, 14 May 2025 15:13:16 -0700
Subject: [PATCH 07/11] move uv to be after venv

---
 content/how-tos/how-to-create-environments.md | 76 +++++++++----------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index 3b078bb..38cd933 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -59,6 +59,44 @@ source science/bin/activate
 You can find more information on using venv for packaging
 [here](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/).
 
+### Set up a virtual environment using uv
+
+To create a new environment using uv in a project folder called `science`,
+navigate to that folder and execute:
+
+```shell
+uv venv
+```
+
+Start using your environment by activating it:
+
+```shell
+source .venv/bin/activate
+```
+
+You are now ready to install Scientific Python packages using `uv`!
+For example:
+
+```shell
+uv pip install ipython numpy scipy
+```
+
+To install dependencies from a requirements file, use:
+
+```shell
+uv pip install -f </path/to/requirements.txt>
+```
+
+Remember to re-activate your environment time you open a new terminal:
+
+```shell
+cd <path/to/science/>
+source .venv/bin/activate
+```
+
+You can find more information on using uv for environments
+[here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
+
 ### Set up an environment using conda
 
 With conda, we can create a new environment named science (-n is the same as passing --name):
@@ -133,44 +171,6 @@ mamba activate science
 You can find more information on using mamba in the
 [mamba user guide](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html).
 
-### Set up a virtual environment using uv
-
-To create a new environment using uv in a project folder called `science`,
-navigate to that folder and execute:
-
-```shell
-uv venv
-```
-
-Start using your environment by activating it:
-
-```shell
-source .venv/bin/activate
-```
-
-You are now ready to install Scientific Python packages using `uv`!
-For example:
-
-```shell
-uv pip install ipython numpy scipy
-```
-
-To install dependencies from a requirements file, use:
-
-```shell
-uv pip install -f </path/to/requirements.txt>
-```
-
-Remember to re-activate your environment time you open a new terminal:
-
-```shell
-cd <path/to/science/>
-source .venv/bin/activate
-```
-
-You can find more information on using uv for environments
-[here](https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment).
-
 ### Set up a virtual environment using pixi
 
 To initialize a new project with pixi in our project called `science`, execute:

From b7a272820c54b206598e47a964452342273a0323 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Wed, 14 May 2025 15:14:49 -0700
Subject: [PATCH 08/11] make venv directions generic

---
 content/how-tos/how-to-create-environments.md | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index 38cd933..8d631a5 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -25,15 +25,16 @@ needed dependencies for a project.
 ### Set up a virtual environment with venv
 
 With venv to create environment associated with a project folder called `science`.
+First, navigate into the `science` project folder. Next, execute: 
 
 ```shell
-python -m venv science
+python -m venv
 ```
 
 Start using it by activating it as follows:
 
 ```shell
-source science/bin/activate
+source .venv/bin/activate
 ```
 
 You are now ready to install Scientific Python packages using `pip`! For example:
@@ -53,7 +54,8 @@ pip install -r <path/to/requirements.txt>
 Remember to re-activate your environment every time you open a new terminal, using:
 
 ```shell
-source science/bin/activate
+cd <path/to/science/>
+source .venv/bin/activate
 ```
 
 You can find more information on using venv for packaging

From 381fb25356e3256802e204adc5ed7da31e241aba Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Wed, 14 May 2025 15:21:09 -0700
Subject: [PATCH 09/11] Update pixi capitalization to refer to project name

Co-authored-by: Matthew Feickert <matthew.feickert@cern.ch>
---
 content/how-tos/how-to-create-environments.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index 8d631a5..aec127c 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -173,9 +173,9 @@ mamba activate science
 You can find more information on using mamba in the
 [mamba user guide](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html).
 
-### Set up a virtual environment using pixi
+### Set up a virtual environment using Pixi
 
-To initialize a new project with pixi in our project called `science`, execute:
+To initialize a new project with Pixi in our project called `science`, execute:
 
 ```shell
 pixi init
@@ -201,7 +201,7 @@ the science folder, and execute:
 pixi shell
 ```
 
-This will drop you into the default environment for the pixi project, with all
+This will drop you into the default environment for the Pixi project, with all
 dependencies in that environment accessible to you in that shell.
 
 A pixi project may have multiple environments defined in the `pixi.toml` file. To

From 0563d47ef5d7ae28860cda498f2a29b7ffa34465 Mon Sep 17 00:00:00 2001
From: Madicken Munk <madicken.munk@gmail.com>
Date: Wed, 14 May 2025 15:22:06 -0700
Subject: [PATCH 10/11] update pixi directions for clarity

Co-authored-by: Matthew Feickert <matthew.feickert@cern.ch>
---
 content/how-tos/how-to-create-environments.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index aec127c..7e59f4a 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -182,13 +182,13 @@ pixi init
 ```
 
 You are now ready to install Scientific Python packages as dependencies in this project!
-From the science directory, execute:
+From the `science` directory, execute:
 
 ```shell
 pixi add ipython numpy scipy
 ```
 
-To install dependencies from a file like `environment.yml`, use:
+If you have an existing conda environment defined in an `environment.yml`, you can initialize a Pixi environment with the packages defined in it by executing:
 
 ```shell
 pixi init --import <path/to/environment.yml>

From ba8e25d9058ad99216c0eb1812332bd949aff869 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 14 May 2025 22:22:30 +0000
Subject: [PATCH 11/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 content/how-tos/how-to-create-environments.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/how-tos/how-to-create-environments.md b/content/how-tos/how-to-create-environments.md
index 7e59f4a..5186d80 100644
--- a/content/how-tos/how-to-create-environments.md
+++ b/content/how-tos/how-to-create-environments.md
@@ -25,7 +25,7 @@ needed dependencies for a project.
 ### Set up a virtual environment with venv
 
 With venv to create environment associated with a project folder called `science`.
-First, navigate into the `science` project folder. Next, execute: 
+First, navigate into the `science` project folder. Next, execute:
 
 ```shell
 python -m venv