From 2ebf7d48e82b8546a1a56fe08978e79581192267 Mon Sep 17 00:00:00 2001
From: Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
Date: Mon, 18 Mar 2024 10:06:25 +0000
Subject: [PATCH] WIP: updating installation instructions/environments.

---
 envs/README.md                       | 20 ++++++++++++
 envs/{windows.yml => linux-full.yml} |  0
 envs/m1-mac.yml                      |  2 +-
 envs/m2-mac.yml                      |  2 +-
 envs/mac-full.yml                    | 46 ++++++++++++++++++++++++++++
 5 files changed, 68 insertions(+), 2 deletions(-)
 create mode 100644 envs/README.md
 rename envs/{windows.yml => linux-full.yml} (100%)
 create mode 100644 envs/mac-full.yml

diff --git a/envs/README.md b/envs/README.md
new file mode 100644
index 00000000..85d2e517
--- /dev/null
+++ b/envs/README.md
@@ -0,0 +1,20 @@
+Conda Environments
+------------------
+
+See the official documentation for the [installation instructions]().
+
+OSL only environments:
+
+- `linux-generic.yml`: most generic environment for linux computers.
+- `bmrc.yml`: for the Oxford BMRC cluster.
+- `hbaws.yml`: for the OHBA workstation. Comes with Spyder.
+- `m1-mac.yml`: for M1 Macs. Comes with Spyder.
+- `m2-mac.yml`: for M2 Macs. Comes with Spyder.
+
+OSL + osl-dynamics environments:
+
+- **`linux.yml`: recommended environment for linux computers.**
+- **`mac.yml`: recommended environment for Mac computers.**
+- `osl-workshop-23.yml`: used in the [2023 OSL Workshop](https://osf.io/zxb6c/).
+
+All environments come with Jupyter Notebook.
diff --git a/envs/windows.yml b/envs/linux-full.yml
similarity index 100%
rename from envs/windows.yml
rename to envs/linux-full.yml
diff --git a/envs/m1-mac.yml b/envs/m1-mac.yml
index 8c54a66d..eeab01bd 100644
--- a/envs/m1-mac.yml
+++ b/envs/m1-mac.yml
@@ -277,7 +277,7 @@ dependencies:
    - rfc3986-validator==0.1.1
    - rope==1.7.0
    - rtree==1.0.1
-   - sails==1.4.0
+   - sails==1.6.0
    - scikit-learn==1.2.2
    - scipy==1.10.1
    - send2trash==1.8.0
diff --git a/envs/m2-mac.yml b/envs/m2-mac.yml
index 1335de17..58afdde8 100644
--- a/envs/m2-mac.yml
+++ b/envs/m2-mac.yml
@@ -337,7 +337,7 @@ dependencies:
     - pyviz-comms==2.2.1
     - rfc3339-validator==0.1.4
     - rfc3986-validator==0.1.1
-    - sails==1.4.0
+    - sails==1.6.0
     - scikit-learn==1.2.2
     - scipy==1.10.1
     - send2trash==1.8.0
diff --git a/envs/mac-full.yml b/envs/mac-full.yml
new file mode 100644
index 00000000..ad86f395
--- /dev/null
+++ b/envs/mac-full.yml
@@ -0,0 +1,46 @@
+name: osl
+channels:
+- conda-forge
+dependencies:
+- python=3.8.16
+- pip=23.0.1
+- vtk=9.1.0=*osmesa*
+- pyvista=0.38.5
+- pip:
+  - jupyter==1.0.0
+  - ipympl==0.9.3
+  - ipywidgets==8.0.5
+  - ipyevents==2.0.1
+  - ipyvtklink==0.2.2
+  - jupyter-client==8.1.0
+  - numpy==1.23.5
+  - scipy==1.10.1
+  - matplotlib==3.7.1
+  - mne==1.3.1
+  - scikit-learn==1.2.2
+  - fslpy==3.11.3
+  - sails==1.4.0
+  - tabulate==0.9.0
+  - pyyaml==6.0
+  - neurokit2==0.2.3
+  - jinja2==3.1.2
+  - glmtools==0.2.1
+  - numba==0.56.4
+  - nilearn==0.10.2
+  - dask==2023.3.2
+  - distributed==2023.3.2
+  - parse==1.19.0
+  - opencv-python==4.7.0.72
+  - h5io==0.1.7
+  - mat73==0.60
+  - nibabel==5.0.1
+  - pandas==1.5.3
+  - panel==1.2.3
+  - pqdm==0.2.0
+  - seaborn==0.12.2
+  - tensorflow-macos==2.9.1
+  - tensorflow_probability==0.17.0
+  - tqdm==4.65.0
+  - osfclient==0.0.5
+  - osl
+  - osl-dynamics