From 757ce33b4e6f5c275e31b67d32ddb57c7b44b721 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Wed, 13 Mar 2024 11:08:45 -0400
Subject: [PATCH 01/17] change default fft to scipy

---
 src/aspire/config_default.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/aspire/config_default.yaml b/src/aspire/config_default.yaml
index 3d135a64f6..2a7725b1a2 100644
--- a/src/aspire/config_default.yaml
+++ b/src/aspire/config_default.yaml
@@ -3,7 +3,7 @@ common:
     # numeric module to use - one of numpy/cupy
     numeric: numpy
     # fft backend to use - one of pyfftw/scipy/cupy/mkl
-    fft: pyfftw
+    fft: scipy
 
     # Set cache directory for ASPIRE example data.
     # By default the cache location will be set by pooch.os_cache(),

From cb87c35a9ffb4cf53c6b2f61c26869ffd9b4ce2e Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Wed, 13 Mar 2024 11:09:11 -0400
Subject: [PATCH 02/17] remove pyfftw from depends

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0e28ebad97..478e1fe0dc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,7 +44,6 @@ dependencies = [
     "pooch>=1.7.0",
     "pillow",
     "psutil",
-    "pyfftw",
     "pymanopt",
     "pyshtools<=4.10.4",  # 4.11.7 might have a packaging bug
     "PyWavelets",

From 14f7e8795bd8350a408b87c067e37a872d1587f8 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Wed, 13 Mar 2024 11:17:02 -0400
Subject: [PATCH 03/17] remove pyfftw from environment yamls

---
 environment-accelerate.yml | 4 ----
 environment-default.yml    | 4 ----
 environment-intel.yml      | 4 ----
 environment-openblas.yml   | 4 ----
 4 files changed, 16 deletions(-)

diff --git a/environment-accelerate.yml b/environment-accelerate.yml
index 1d01c51d75..1a0a6c9e5a 100644
--- a/environment-accelerate.yml
+++ b/environment-accelerate.yml
@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5
diff --git a/environment-default.yml b/environment-default.yml
index f092f4c3ca..f5ff7ae893 100644
--- a/environment-default.yml
+++ b/environment-default.yml
@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5
diff --git a/environment-intel.yml b/environment-intel.yml
index fa3beba787..83250caeaf 100644
--- a/environment-intel.yml
+++ b/environment-intel.yml
@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5
diff --git a/environment-openblas.yml b/environment-openblas.yml
index bc4d61b46d..ee2f665e6e 100644
--- a/environment-openblas.yml
+++ b/environment-openblas.yml
@@ -5,10 +5,6 @@ channels:
   - defaults
 
 dependencies:
-  - fftw
-  # There is a potential pyFFTW bug, pin to 0.12
-  #   https://github.com/pyFFTW/pyFFTW/issues/294
-  - pyfftw=0.12
   - pip
   - python=3.8
   - numpy=1.23.5

From 9a2023c4d7bfe424e8f6338c33209b41fef93b47 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Wed, 13 Mar 2024 11:17:22 -0400
Subject: [PATCH 04/17] Emit message to install pyfftw to use as a backend

---
 src/aspire/numeric/pyfftw_fft.py |  6 +++++-
 tests/test_fft.py                | 12 +++++++++++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/aspire/numeric/pyfftw_fft.py b/src/aspire/numeric/pyfftw_fft.py
index c1b183108a..9cfdd45210 100644
--- a/src/aspire/numeric/pyfftw_fft.py
+++ b/src/aspire/numeric/pyfftw_fft.py
@@ -1,7 +1,11 @@
 import os
 from threading import Lock
 
-import pyfftw
+try:
+    import pyfftw
+except ModuleNotFoundError:
+    raise ModuleNotFoundError("Install `pyfftw` to use as a backend.")
+
 import pyfftw.interfaces.scipy_fftpack as scipy_fft
 
 from aspire.numeric.base_fft import FFT
diff --git a/tests/test_fft.py b/tests/test_fft.py
index 45f22b1fd1..5a88929402 100644
--- a/tests/test_fft.py
+++ b/tests/test_fft.py
@@ -1,3 +1,4 @@
+import logging
 from unittest import TestCase
 
 import numpy as np
@@ -5,8 +6,17 @@
 from aspire import config
 from aspire.numeric import fft_object, numeric_object
 
+logger = logging.getLogger(__name__)
 # Create test option combinations between numerical modules and FFT libs
-test_backends = [("numpy", "scipy"), ("numpy", "pyfftw")]
+test_backends = [("numpy", "scipy")]
+
+try:
+    import pyfftw  # noqa: F401
+
+    test_backends.append(("numpy", "pyfftw"))
+except ModuleNotFoundError:
+    logger.info("`pyfftw` module is not installed, skipping `pyfftw` FFT backend.")
+
 
 # Create Cupy fft backend if Cupy module is enabled and lib exits.
 if config["common"]["numeric"].as_str() == "cupy":

From 6439b93ef4284891962e6868d4eb74199d880b2f Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Wed, 5 Jun 2024 16:15:13 -0400
Subject: [PATCH 05/17] attempt adding osx m1 runner

---
 .github/workflows/workflow.yml | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 64dfa54961..81494105ac 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -4,7 +4,7 @@ on:
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
   push:
-  
+
 
 jobs:
   check:
@@ -215,3 +215,19 @@ jobs:
           name: sphinx-docs
           path: docs/build
           retention-days: 7
+
+  osx_arm:
+    needs: check
+    runs-on: macos-latest-xlarge
+    # Run on every code push, but only on review ready PRs
+    if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: pip install tox tox-gh-actions
+    - name: Test
+      run: python -m pytest --durations=50

From ee6c57007f37a5819263a03b96a20339880bef8f Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Thu, 6 Jun 2024 08:53:28 -0400
Subject: [PATCH 06/17] mac osx latest to 14

---
 .github/workflows/workflow.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 81494105ac..92e68dfd28 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -218,7 +218,7 @@ jobs:
 
   osx_arm:
     needs: check
-    runs-on: macos-latest-xlarge
+    runs-on: macos-14
     # Run on every code push, but only on review ready PRs
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
     steps:

From 722ef87d20ae7090785d488ec3a0ed324f72361c Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Thu, 6 Jun 2024 08:58:21 -0400
Subject: [PATCH 07/17] install deps

---
 .github/workflows/workflow.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 92e68dfd28..57bf288dd2 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -228,6 +228,8 @@ jobs:
       with:
         python-version: '3.8'
     - name: Install dependencies
-      run: pip install tox tox-gh-actions
+      run: |
+           pip install tox tox-gh-actions
+           pip install -e ".[dev]"
     - name: Test
       run: python -m pytest --durations=50

From 47f9a4c1ad04a9a6623c42ed8565460c554b407d Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Thu, 6 Jun 2024 15:51:25 -0400
Subject: [PATCH 08/17] attempt pre-installing pyshtools via conda

---
 .github/workflows/workflow.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 57bf288dd2..d6dc83bf19 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -223,13 +223,18 @@ jobs:
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v2.3.0
       with:
+        miniconda-version: "latest"
+        auto-update-conda: true
         python-version: '3.8'
-    - name: Install dependencies
+    - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
       run: |
-           pip install tox tox-gh-actions
-           pip install -e ".[dev]"
+        conda info
+        conda list
+        conda install pyshtools  # debug depends issues
+        pip install -e ".[dev]"  # install aspire
+        pip freeze
     - name: Test
       run: python -m pytest --durations=50

From f1cc12f8eb650aa84dd4d19ec124a5c505b394d9 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Thu, 6 Jun 2024 15:59:31 -0400
Subject: [PATCH 09/17] attempt pre-installing pyshtools via conda env

---
 .github/workflows/workflow.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index d6dc83bf19..bf3f86a308 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -229,6 +229,9 @@ jobs:
         miniconda-version: "latest"
         auto-update-conda: true
         python-version: '3.8'
+        activate-environment: aspire
+        environment-file: environment-accelerate.yml
+        auto-activate-base: false
     - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
       run: |
         conda info

From 57bc7bb623675c6a119a851af395287aba6df201 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Fri, 7 Jun 2024 09:58:33 -0400
Subject: [PATCH 10/17] use base env and shell

---
 .github/workflows/workflow.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index bf3f86a308..3003839e4e 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -22,7 +22,7 @@ jobs:
       run: tox -e check
 
   build:
-    needs: check
+    needs: osx_arm
     runs-on: ubuntu-latest
     # Run on every code push, but only on review ready PRs
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}    
@@ -55,7 +55,7 @@ jobs:
       uses: codecov/codecov-action@v4
 
   conda-build:
-    needs: check
+    needs: osx_arm
     runs-on: ${{ matrix.os }}
     # Only run on review ready pull_requests
     if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
@@ -121,7 +121,7 @@ jobs:
       shell: bash
 
   ampere_gpu:
-    needs: check
+    needs: osx_arm
     runs-on: self-hosted
     # Run on every code push, but only on review ready PRs
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
@@ -217,6 +217,9 @@ jobs:
           retention-days: 7
 
   osx_arm:
+    defaults:
+      run:
+        shell: bash -l {0}
     needs: check
     runs-on: macos-14
     # Run on every code push, but only on review ready PRs
@@ -228,10 +231,9 @@ jobs:
       with:
         miniconda-version: "latest"
         auto-update-conda: true
+        channels: conda-forge, defaults
         python-version: '3.8'
-        activate-environment: aspire
-        environment-file: environment-accelerate.yml
-        auto-activate-base: false
+        auto-activate-base: true
     - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
       run: |
         conda info

From 94bcfbc0371cbfd9af5dcf92724ed9bebb0b658c Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Fri, 7 Jun 2024 10:55:46 -0400
Subject: [PATCH 11/17] try updated accel env

---
 .github/workflows/workflow.yml | 5 +++--
 environment-accelerate.yml     | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 3003839e4e..a96d6b05bd 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -231,9 +231,10 @@ jobs:
       with:
         miniconda-version: "latest"
         auto-update-conda: true
-        channels: conda-forge, defaults
         python-version: '3.8'
-        auto-activate-base: true
+        activate-environment: aspire
+        environment-file: environment-accelerate.yml
+        auto-activate-base: false
     - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
       run: |
         conda info
diff --git a/environment-accelerate.yml b/environment-accelerate.yml
index 1a0a6c9e5a..38dd49813d 100644
--- a/environment-accelerate.yml
+++ b/environment-accelerate.yml
@@ -7,8 +7,9 @@ channels:
 dependencies:
   - pip
   - python=3.8
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - pyshtools
+  - numpy=1.24.1
+  - scipy=1.10.1
   - scikit-learn
   - scikit-image
   - libblas=*=*accelerate

From 2c77825b0dc5ab3732553a820de9e1bbeb8e8de2 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Fri, 7 Jun 2024 12:06:50 -0400
Subject: [PATCH 12/17] restore job deps, and try parallel for osx_arm

---
 .github/workflows/workflow.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index a96d6b05bd..ffe85d5343 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -22,7 +22,7 @@ jobs:
       run: tox -e check
 
   build:
-    needs: osx_arm
+    needs: check
     runs-on: ubuntu-latest
     # Run on every code push, but only on review ready PRs
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}    
@@ -55,7 +55,7 @@ jobs:
       uses: codecov/codecov-action@v4
 
   conda-build:
-    needs: osx_arm
+    needs: check
     runs-on: ${{ matrix.os }}
     # Only run on review ready pull_requests
     if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
@@ -121,7 +121,7 @@ jobs:
       shell: bash
 
   ampere_gpu:
-    needs: osx_arm
+    needs: check
     runs-on: self-hosted
     # Run on every code push, but only on review ready PRs
     if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
@@ -243,4 +243,4 @@ jobs:
         pip install -e ".[dev]"  # install aspire
         pip freeze
     - name: Test
-      run: python -m pytest --durations=50
+      run: python -m pytest -n2 --durations=50

From 57e4bbc3eb0e023e1af29391883b7c8c65a141e8 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Fri, 7 Jun 2024 13:47:12 -0400
Subject: [PATCH 13/17] try -n3

---
 .github/workflows/workflow.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index ffe85d5343..6e77dad75e 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -243,4 +243,4 @@ jobs:
         pip install -e ".[dev]"  # install aspire
         pip freeze
     - name: Test
-      run: python -m pytest -n2 --durations=50
+      run: python -m pytest -n3 --durations=50

From 132c378ab0b12b7ac1c1905c0eaec1866c587c80 Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Mon, 10 Jun 2024 11:13:43 -0400
Subject: [PATCH 14/17] continue testing pyfftw backend

---
 .github/workflows/workflow.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 6e77dad75e..06b8dd71af 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -18,6 +18,8 @@ jobs:
     - name: Install dependencies
       run: |
         pip install tox tox-gh-actions
+        # Optional packages
+        pip install pyfftw  # `test_fft` runs for pyfftw when installed
     - name: Run Tox Check
       run: tox -e check
 

From a25fe7d82ffa962743ae079f42fcd7dbc8b3d7a1 Mon Sep 17 00:00:00 2001
From: Marc <mkarim117@berkeley.edu>
Date: Fri, 14 Jun 2024 09:37:44 -0700
Subject: [PATCH 15/17] adjust tolerance for m1

---
 tests/test_synthetic_volume.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_synthetic_volume.py b/tests/test_synthetic_volume.py
index 8860b3532d..ddcdcbcab5 100644
--- a/tests/test_synthetic_volume.py
+++ b/tests/test_synthetic_volume.py
@@ -136,4 +136,4 @@ def test_volume_symmetry(vol_fixture):
         corr = np.dot(rot_vol[0].flatten(), vol[0].flatten()) / np.dot(
             vol[0].flatten(), vol[0].flatten()
         )
-        assert abs(corr - 1) < 1e-5
+        assert abs(corr - 1) < 1.1e-5

From 48aeab2d2b3d7dde438935c0143a112ef4f1e41c Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Mon, 17 Jun 2024 13:33:17 -0400
Subject: [PATCH 16/17] put pyfftw install into correct job

---
 .github/workflows/workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 06b8dd71af..f2d5472e52 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -18,8 +18,6 @@ jobs:
     - name: Install dependencies
       run: |
         pip install tox tox-gh-actions
-        # Optional packages
-        pip install pyfftw  # `test_fft` runs for pyfftw when installed
     - name: Run Tox Check
       run: tox -e check
 
@@ -51,6 +49,8 @@ jobs:
     - name: Install dependencies
       run: |
         pip install tox tox-gh-actions
+        # Optional packages
+        pip install pyfftw  # `test_fft` runs for pyfftw when installed
     - name: Test with tox
       run: tox --skip-missing-interpreters false -e py${{ matrix.python-version }}-${{ matrix.pyenv }}
     - name: Upload Coverage to CodeCov

From 0db87ba60e5ee88b45ed4209ecd1423967c1814d Mon Sep 17 00:00:00 2001
From: Garrett Wright <garrettwrong@gmail.com>
Date: Mon, 17 Jun 2024 13:47:30 -0400
Subject: [PATCH 17/17] Force numpy<2

Numpy Was previously bound <2 by pyfftw deps.
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 478e1fe0dc..f48de5f41b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ dependencies = [
     "joblib",
     "matplotlib >= 3.2.0",
     "mrcfile",
-    "numpy>=1.21.5",
+    "numpy>=1.21.5, <2.0.0",
     "packaging",
     "pooch>=1.7.0",
     "pillow",