From e6686ea1476cfb220d5529b8ce35231ecbcd5cfc Mon Sep 17 00:00:00 2001
From: Simon Mathis <simon.mathis@gmail.com>
Date: Mon, 25 Nov 2024 06:33:39 -0800
Subject: [PATCH] docs: add contributing instructions

---
 .env.sample     |  3 +++
 CONTRIBUTING.md | 45 +++++++++++++++++++++++++++++++++++++++++++++
 CONTRIBUTORS.md | 10 ----------
 README.md       |  4 ++++
 contribute.sh   |  4 ++++
 environment.yml | 19 +++++++++++++++++++
 6 files changed, 75 insertions(+), 10 deletions(-)
 create mode 100644 .env.sample
 create mode 100644 CONTRIBUTING.md
 delete mode 100644 CONTRIBUTORS.md
 create mode 100644 contribute.sh
 create mode 100644 environment.yml

diff --git a/.env.sample b/.env.sample
new file mode 100644
index 0000000..3e1563d
--- /dev/null
+++ b/.env.sample
@@ -0,0 +1,3 @@
+PYMOL_RPC_HOST=localhost
+PYMOL_RPC_PORT=9123
+LOG_LEVEL=INFO
\ No newline at end of file
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..4ba8af1
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,45 @@
+# Contributors
+
+## Special thanks for all the people who have helped this project so far:
+
+* [Simon Mathis](https://github.com/Croydon-Brixton)
+* [Martin Buttenschön](https://github.com/maabuu)
+
+## I would like to join this list. How can I help the project?
+
+We always welcome contributions to improve the project. Please have a look at the current github issues for information on where help could be needed.
+
+### Getting set up:
+The development environment for pymol-remote is detailed in the [`environment.yml` file](environment.yml).
+
+For simplicity, you can set up the development environment using the `contribute.sh` script:
+
+```bash
+# NOTE: If you wish to use a different package manager than conda/etc. you can manually install the dependencies and set the .env file
+./contribute.sh
+```
+
+You can then set the environment variables such as your localhosts's IP address in the `.env` file. Do not commit this file to github.
+
+### Running the tests
+
+To run the tests, you can use
+
+```bash
+# Run all tests
+pytest tests/
+
+# Run only the tests that do not require a running server
+pytest tests/ -m "not requires_server"
+
+# Run only the tests that do not require biotite on the client side
+pytest tests/ -m "not client_requires_biotite"
+
+```
+
+### Test Categories
+
+The test suite uses pytest markers to organize tests:
+
+- `requires_server`: Tests that need a running PyMOL server
+- `client_requires_biotite`: Tests that need biotite installed on the client side
diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
deleted file mode 100644
index f633c7d..0000000
--- a/CONTRIBUTORS.md
+++ /dev/null
@@ -1,10 +0,0 @@
-# Contributors
-
-## Special thanks for all the people who have helped this project so far:
-
-* [Simon Mathis](https://github.com/Croydon-Brixton)
-* [Martin Buttenschön](https://github.com/maabuu)
-
-## I would like to join this list. How can I help the project?
-
-We always welcome contributions to improve the project. Please have a look at the current github issues for information on where help could be needed.
\ No newline at end of file
diff --git a/README.md b/README.md
index 5cfe4df..f6cc287 100644
--- a/README.md
+++ b/README.md
@@ -66,3 +66,7 @@ This implementation is inspired by and based on the original [RDKit RPC](https:/
 
 ## 4. License
 This code is licensed under the same terms as PyMOL. See [LICENSE](./LICENSE) for more details.
+
+
+## 5. Contributing
+See [CONTRIBUTING.md](./CONTRIBUTING.md) for more details.
diff --git a/contribute.sh b/contribute.sh
new file mode 100644
index 0000000..b43acc2
--- /dev/null
+++ b/contribute.sh
@@ -0,0 +1,4 @@
+cp .env.sample .env
+conda env create -f environment.yml
+conda activate pymol-remote
+pytest tests/
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..b00f205
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,19 @@
+name: pymol-remote  # development environment for pymol-remote
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.10
+
+  - pymol-open-source
+  - pytest>=8.3.0,<9.0.0
+
+  - pip
+  - pip:
+    - biotite>=1.0
+    - ruff>=0.8.0,<0.9.0
+    - pytest-dotenv>=0.5.2
+    # ... install pymol-remote in editable mode
+    - -e .