From 92178e4250eb128bfd9c36a7006222022e0a13df Mon Sep 17 00:00:00 2001
From: fynnbe <thefynnbe@gmail.com>
Date: Tue, 12 Mar 2024 16:32:59 +0100
Subject: [PATCH] update dev envs

---
 dev/env.yaml                   | 11 +++++++----
 dev/environment-base.yaml      | 20 +++++++++++++-------
 dev/environment-tf-legacy.yaml | 12 +++++++++---
 dev/environment-tf.yaml        | 12 +++++++++---
 dev/environment-torch.yaml     | 17 +++++++++++------
 5 files changed, 49 insertions(+), 23 deletions(-)

diff --git a/dev/env.yaml b/dev/env.yaml
index 7ee582f5..78ed1f8d 100644
--- a/dev/env.yaml
+++ b/dev/env.yaml
@@ -4,24 +4,27 @@ channels:
   - defaults
 dependencies:
   - annotated-types
+  - bioimageio.spec==0.5.*
   - black
   - deepdiff
   - email-validator
-  - imageio[version='>=2.5']
+  - filelock
+  - imageio>=2.5
+  - loguru
   - lxml
   - numpy
   - onnxruntime
-  - packaging[version='>=17.0']
+  - packaging>=17.0
   - pooch
   - pre-commit
-  - pydantic[version='>=2.3.0']
+  - pydantic>=2.6.4
   - pyright
   - pytest
   - python-dateutil
   - python=3.8
   - pytorch
-  - ruyaml
   - ruff
+  - ruyaml
   - torchvision
   - tqdm
   - typer
diff --git a/dev/environment-base.yaml b/dev/environment-base.yaml
index 88a336ee..96a96d91 100644
--- a/dev/environment-base.yaml
+++ b/dev/environment-base.yaml
@@ -3,20 +3,26 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - bioimageio.spec==0.5.*
   - black
-  - bioimageio.spec
   - conda-build
+  - filelock
   - h5py >=2.10,<2.11
+  - loguru
   - mypy
+  - onnx
+  - onnxruntime
   - pip
   - pre-commit
+  - psutil
   - pytest
-  - python >=3.7,<3.8  # this environment is only available for python 3.7
-  - xarray
+  - pytest-xdist
+  - python >=3.7,<3.8 # this environment is only available for python 3.7
   - pytorch
-  - onnx
-  - onnxruntime
+  - ruyaml
   - tensorflow >=1.12,<2.0
-  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - tifffile <=2022.4.8 # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - typer
+  - xarray
   - pip:
-    - keras==1.2.2
+      - keras==1.2.2
diff --git a/dev/environment-tf-legacy.yaml b/dev/environment-tf-legacy.yaml
index 976ea3d6..d1bbbc28 100644
--- a/dev/environment-tf-legacy.yaml
+++ b/dev/environment-tf-legacy.yaml
@@ -4,14 +4,20 @@ channels:
   - defaults
 dependencies:
   - black
-  - bioimageio.spec
+  - bioimageio.spec==0.5.*
   - conda-build
   - h5py >=2.10,<2.11
   - mypy
   - pip
   - pytest
-  - python >=3.7,<3.8  # this environment is only available for python 3.7
+  - pytest-xdist
+  - filelock
+  - psutil
+  - python >=3.7,<3.8 # this environment is only available for python 3.7
   - xarray
   - tensorflow >1.14,<2.0
-  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - tifffile <=2022.4.8 # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
   - keras
+  - ruyaml
+  - typer
+  - loguru
diff --git a/dev/environment-tf.yaml b/dev/environment-tf.yaml
index 4ecd57d8..03c6b08b 100644
--- a/dev/environment-tf.yaml
+++ b/dev/environment-tf.yaml
@@ -3,13 +3,19 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - bioimageio.spec==0.5.*
   - black
-  - bioimageio.spec
   - conda-build
+  - filelock
+  - loguru
   - mypy
   - pip
+  - psutil
   - pytest
+  - pytest-xdist
   - python
-  - xarray
+  - ruyaml
   - tensorflow >=2.9,<3.0
-  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - tifffile <=2022.4.8 # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - typer
+  - xarray
diff --git a/dev/environment-torch.yaml b/dev/environment-torch.yaml
index 98a944cd..c97a8225 100644
--- a/dev/environment-torch.yaml
+++ b/dev/environment-torch.yaml
@@ -3,17 +3,22 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - bioimageio.spec==0.5.*
   - black
-  - bioimageio.spec >=0.4.4
   - conda-build
+  - filelock
   - h5py
+  - loguru
   - mypy
+  - onnx
+  - onnxruntime
   - pip
+  - psutil
   - pytest
+  - pytest-xdist
   - python >=3.7
-  - xarray
   - pytorch
-  - onnx
-  - onnxruntime
-  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
-
+  - ruyaml
+  - tifffile <=2022.4.8 # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+  - typer
+  - xarray