5596 simplify conda env (#5597)

Fixes #5596
Fixes #5088

### Description
simplify the conda env

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Author: wyli

.github/workflows/conda.yml

@@ -18,8 +18,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: ["3.8"]
+        os: [windows-latest, ubuntu-latest]
+        python-version: ["3.9"]
     runs-on: ${{ matrix.os }}
     env:
       QUICKTEST: True

docs/source/installation.md

@@ -203,7 +203,8 @@ cd MONAI/
 pip install -r requirements-dev.txt
 ```
 
-To install all optional dependencies with `conda` based on MONAI development environment settings:
+To install all optional dependencies with `conda` based on MONAI development environment settings (`environment-dev.yml`;
+this will install PyTorch as well as `pytorch-cuda`, please follow https://pytorch.org/get-started/locally/#start-locally for more details about installing PyTorch):
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/

environment-dev.yml

@@ -2,66 +2,13 @@ name: monai
 channels:
   - pytorch
   - defaults
+  - nvidia
   - conda-forge
 dependencies:
   - numpy>=1.17
   - pytorch>=1.8
-  - coverage>=5.5
-  - parameterized
-  - setuptools>=50.3.0,!=60.0.0
-  - ignite==0.4.10
-  - gdown>=4.4.0
-  - scipy
-  - nibabel
-  - pillow!=8.3.0 # https://github.com/python-pillow/Pillow/issues/5571
-  - tensorboard
-  - scikit-image>=0.14.2
-  - tqdm>=4.47.0
-  - python-lmdb
-  - flake8>=3.8.1
-  - flake8-bugbear
-  - flake8-comprehensions
-  - pylint
-  - mccabe
-  - pep8-naming
-  - pycodestyle
-  - pyflakes
-  - isort
-  - types-pkg_resources
-  - ninja
   - torchvision
-  - psutil
-  - Sphinx==3.5.3
-  - recommonmark==0.6.0
-  - sphinx-autodoc-typehints==1.11.1
-  - sphinx_rtd_theme==0.5.2
-  - pandas
-  - requests
-  - einops
-  - transformers<4.22  # https://github.com/Project-MONAI/MONAI/issues/5157
-  - mlflow
-  - tensorboardX
-  - pyyaml
-  - fire
-  - jsonschema
-  - pynrrd
-  - pydicom
-  - h5py
-  - optuna
+  - pytorch-cuda=11.6
   - pip
   - pip:
-    # pip for itk as conda-forge version only up to v5.1
-    - itk>=5.2
-    # black currently at v19 on conda vs v21 on pip
-    - black
-    # conda mypy v. slow
-    - mypy>=0.790
-    # OS-specific needs to be done via pip:
-    #   https://github.com/conda/conda/issues/8089
-    - pytype>=2020.6.1; platform_system != "Windows"
-    - openslide-python==1.1.2
-    - cucim>=22.8.1; platform_system == "Linux"
-    - imagecodecs; platform_system == "Linux"
-    - tifffile; platform_system == "Linux"
-    - matplotlib!=3.5.0
-    - nni
+    - -r requirements-dev.txt

tests/test_attentionunet.py

@@ -14,7 +14,7 @@
 import torch
 
 import monai.networks.nets.attentionunet as att
-from tests.utils import skip_if_no_cuda
+from tests.utils import skip_if_no_cuda, skip_if_quick
 
 
 class TestAttentionUnet(unittest.TestCase):
@@ -34,6 +34,7 @@ def test_attention_block(self):
             output = block(g, x)
             self.assertEqual(output.shape, x.shape)
 
+    @skip_if_quick
     def test_attentionunet(self):
         for dims in [2, 3]:
             shape = (3, 1) + (92,) * dims

tests/test_unetr.py

@@ -16,7 +16,7 @@
 
 from monai.networks import eval_mode
 from monai.networks.nets.unetr import UNETR
-from tests.utils import SkipIfBeforePyTorchVersion, test_script_save
+from tests.utils import SkipIfBeforePyTorchVersion, skip_if_quick, test_script_save
 
 TEST_CASE_UNETR = []
 for dropout_rate in [0.4]:
@@ -53,6 +53,7 @@
                                             TEST_CASE_UNETR.append(test_case)
 
 
+@skip_if_quick
 class TestUNETR(unittest.TestCase):
     @parameterized.expand(TEST_CASE_UNETR)
     def test_shape(self, input_param, input_shape, expected_shape):