From 22bba6a51c656a4ec347bf009a64cb4967cc2f63 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Fri, 8 Dec 2023 14:57:36 -0500
Subject: [PATCH 1/4] update instructions for dev environment setup

---
 docs/cli.md | 33 ++++++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 9bc9060a..f39fc672 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -152,11 +152,34 @@ Neurobagel is under active, early development and future releases of the CLI may
 _If you have already created `.jsonld` files for your Neurobagel graph database using the CLI_, 
 they can be quickly re-generated under the new data model by following the instructions [here](updating_dataset.md#following-a-change-in-the-neurobagel-data-model) so that they will not conflict with dataset `.jsonld` files generated using the latest CLI version.
 
+
 ## Development environment
 
-To set up a development environment, please run
+To ensure that our Docker images are built in a predictable way,
+we use `requirements.txt` as a lock-file.
+That is, `requirements.txt` includes the entire dependency tree of our tool,
+with pinned versions for every dependency (see [also](https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability))
+
+### Setting up a local development environment
+We suggest that you create a development environment 
+that is as close as possible to the environment we run in production.
+
+To do so, we first need to install the dependencies from our lockfile (`dev_requirements.txt`):
+
 ```bash
-git clone https://github.com/neurobagel/bagel-cli.git
-cd bagel-cli
-pip install -e '.[all]'
-```
\ No newline at end of file
+pip install -r dev_requirements.txt
+```
+
+And then we install the CLI without touching the dependencies
+
+```bash
+pip install --no-deps -e .
+```
+
+Finally, to run the test suite we need to install the `bids-examples` and `neurobagel_examples` submodules:
+```bash
+git submodule init
+git submodule update
+```
+Confirm that everything works well by running a test
+`pytest .`

From d33908bd569fdca0d63541d4f12cb07edcb00060 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 13 Dec 2023 21:08:37 -0500
Subject: [PATCH 2/4] recommend installing pre-commit hooks

---
 docs/cli.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/cli.md b/docs/cli.md
index f39fc672..ca0411cc 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -183,3 +183,13 @@ git submodule update
 ```
 Confirm that everything works well by running a test
 `pytest .`
+
+
+#### Setting up code formatting and linting (recommended)
+
+[pre-commit](https://pre-commit.com/) is configured in the development environment for this repository, and can be set up to automatically run a number of code linters and formatters on any commit you make according to the consistent code style set for this project.
+
+Run the following from the repository root to install the configured pre-commit "hooks" for your local clone of the repo:
+```bash
+pre-commit install
+```

From 58827d751d4cd0eb58f0c197229fb5984341e57c Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 13 Dec 2023 21:15:56 -0500
Subject: [PATCH 3/4] clarify dev env setup

---
 docs/cli.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index ca0411cc..67c85a74 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -158,7 +158,7 @@ they can be quickly re-generated under the new data model by following the instr
 To ensure that our Docker images are built in a predictable way,
 we use `requirements.txt` as a lock-file.
 That is, `requirements.txt` includes the entire dependency tree of our tool,
-with pinned versions for every dependency (see [also](https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability))
+with pinned versions for every dependency (for more information, see [https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability](https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability)).
 
 ### Setting up a local development environment
 We suggest that you create a development environment 
@@ -182,7 +182,8 @@ git submodule init
 git submodule update
 ```
 Confirm that everything works well by running a test
-`pytest .`
+`pytest .` 
+(no tests should fail).
 
 
 #### Setting up code formatting and linting (recommended)

From d51950b795655f45b0fff14d415234cb12591cb7 Mon Sep 17 00:00:00 2001
From: Alyssa Dai <alyssa.ydai@gmail.com>
Date: Wed, 13 Dec 2023 21:19:12 -0500
Subject: [PATCH 4/4] grammar fix

---
 docs/cli.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/cli.md b/docs/cli.md
index 67c85a74..f83f4562 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -181,7 +181,7 @@ Finally, to run the test suite we need to install the `bids-examples` and `neuro
 git submodule init
 git submodule update
 ```
-Confirm that everything works well by running a test
+Confirm that everything works well by running a test:
 `pytest .` 
 (no tests should fail).