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Downgrade jax to 0.4.23 in biomakerca notebooks.
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This is because we are using evojax which needs an old version of flax. Old flax is not compatible with new jax ([see this discussion](google/flax#3180)).

This is a temporary patch. Hopefully. We will figure out how to either fix evojax or stop using it for future experiments.

Also, fix a bug on the sexual reproduction colab where I was importing a function that I deleted, causing the colab to fail.

PiperOrigin-RevId: 638631920
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@oteret
oteret authored and Selforg Gardener committed May 30, 2024
1 parent f188d30 commit 8ff6c23
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/e2e_evolution.ipynb
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"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/eruption_example.ipynb
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Expand Up @@ -38,6 +38,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/evolving_in_small_worlds.ipynb
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Expand Up @@ -40,6 +40,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/interactive_evolution.ipynb
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Expand Up @@ -37,6 +37,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/petri_evolution.ipynb
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Expand Up @@ -36,6 +36,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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23 changes: 23 additions & 0 deletions self_organising_systems/biomakerca/examples/notebooks/run_configuration.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
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24 changes: 23 additions & 1 deletion self_organising_systems/biomakerca/examples/notebooks/run_sexual_configuration.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,29 @@
"## Imports"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "WpvHmJytfxpq"
},
"source": [
"We need to downgrade jax, unfortunately.\n",
"This is because we are using evojax which needs an old version of flax.\n",
"Old flax is not compatible with new jax ([see this discussion](https://github.com/google/flax/issues/3180))."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "JgpxBfCFf7j2"
},
"outputs": [],
"source": [
"# downgrade jax with cuda.\n",
"!pip install \"jax[cuda12_pip]\"==0.4.23 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -74,7 +97,6 @@
"from self_organising_systems.biomakerca.step_maker import step_env\n",
"from self_organising_systems.biomakerca.display_utils import zoom, tile2d, add_text_to_img, imshow\n",
"from self_organising_systems.biomakerca.custom_ipython_display import display\n",
"from self_organising_systems.biomakerca.env_logic import env_perform_multi_world_reproduce_update\n",
"\n",
"import cv2\n",
"import numpy as np\n",
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