From a50e343db5d0fd2c42cc0884e6e8bcbd8d0507f8 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Tue, 18 Jun 2024 09:04:33 -0400
Subject: [PATCH 01/30] update core tests-check numpy 2.0

---
 .github/workflows/core-test.yml | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index f654dcdc1..a06d29e7e 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -26,21 +26,12 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        numpy-version: ['1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4', '2.0']
         exclude:
-           - python-version: '3.8'
-             numpy-version: '1.25.1'
-           - python-version: '3.8'
-             numpy-version: '1.26.4'
-           - python-version: '3.10'
-             numpy-version: '1.20.3'
-           - python-version: '3.11'
-             numpy-version: '1.20.3'
            - python-version: '3.11'
              numpy-version: '1.21.6'
            - python-version: '3.12'
-             numpy-version: '1.20.3'
            # python 3.12 only works on latest numpy
            - python-version: '3.12'
              numpy-version: '1.21.6'

From 9f0c35e940342a23059d57e3f1367fa76a932899 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:16:31 -0400
Subject: [PATCH 02/30] add back in 2.0 test

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

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 07ad95174..9a65d2ccf 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -27,7 +27,7 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4', '2.0']
         exclude:
            - python-version: '3.12'
              numpy-version: '1.22.4'

From dec766732660bf88f0c1a4b783680e93c74b8de8 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:19:51 -0400
Subject: [PATCH 03/30] change dependency for testing

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 40ff91a28..442cfb761 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ classifiers = [
 
 dependencies = [
     "packaging",
-    "numpy>=1.22.4,<2.0.0",
+    "numpy>=1.22.4",
     "quantities>=0.14.1,<0.16.0"
 ]
 

From 5b5c6c005cdc1ad8142856e0c107961242bc30b2 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 11:56:09 -0400
Subject: [PATCH 04/30] update exclusion list for 2.0

---
 .github/workflows/core-test.yml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 9a65d2ccf..9c15f4871 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -27,8 +27,20 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4', '2.0']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4', '2.0', '2.1']
         exclude:
+           - python-version: '3.9'
+             numpy-version: '2.0'
+           - python-version: '3.9'
+             numpy-version: '2.1'
+           - python-version: '3.10'
+             numpy-version: '2.0'
+           - python-version: '3.10'
+             numpy-version: '2.1'
+           - python-version: '3.11'
+             numpy-version: '2.0'
+           - python-version: '3.11'
+             numpy-version: '2.1'
            - python-version: '3.12'
              numpy-version: '1.22.4'
            - python-version: '3.12'
@@ -37,6 +49,7 @@ jobs:
              numpy-version: '1.24.1'
            - python-version: '3.12'
              numpy-version: '1.25.1'
+
     steps:
         - name: Set up Python ${{ matrix.python-version }}
           uses: actions/setup-python@v4

From 24f0e63ef30d8597ba2d2471b6fa99ae1edfda08 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:04:50 -0400
Subject: [PATCH 05/30] add python 3.13

---
 .github/workflows/core-test.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 9c15f4871..4ed4f831c 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -26,20 +26,10 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4', '2.0', '2.1']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0', '2.1']
         exclude:
            - python-version: '3.9'
-             numpy-version: '2.0'
-           - python-version: '3.9'
-             numpy-version: '2.1'
-           - python-version: '3.10'
-             numpy-version: '2.0'
-           - python-version: '3.10'
-             numpy-version: '2.1'
-           - python-version: '3.11'
-             numpy-version: '2.0'
-           - python-version: '3.11'
              numpy-version: '2.1'
            - python-version: '3.12'
              numpy-version: '1.22.4'
@@ -49,6 +39,16 @@ jobs:
              numpy-version: '1.24.1'
            - python-version: '3.12'
              numpy-version: '1.25.1'
+           - python-version: '3.13'
+             numpy-version: '1.22.4'
+           - python-version: '3.13'
+             numpy-version: '1.23.5'
+           - python-version: '3.13'
+             numpy-version: '1.24.1'
+           - python-version: '3.13'
+             numpy-version: '1.25.1'
+           - python-version: '3.13'
+             numpy-version: '1.26.4'
 
     steps:
         - name: Set up Python ${{ matrix.python-version }}

From 3bcbe1cb68e82347b277f2ba142ab0fab3bb6282 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:06:44 -0400
Subject: [PATCH 06/30] oops

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

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 4ed4f831c..1fe361619 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -36,7 +36,7 @@ jobs:
            - python-version: '3.12'
              numpy-version: '1.23.5'
            - python-version: '3.12'
-             numpy-version: '1.24.1'
+             numpy-version: '1.24.4'
            - python-version: '3.12'
              numpy-version: '1.25.1'
            - python-version: '3.13'

From a22c61b06cd42a36f551491f5f38df1efbb823ad Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:09:26 -0400
Subject: [PATCH 07/30] no 2.1 for now

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

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 1fe361619..b1b03dac3 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -27,7 +27,7 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0', '2.1']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0',]
         exclude:
            - python-version: '3.9'
              numpy-version: '2.1'

From 5dc0dc8dd10291c9862e223d5ff93134eac6af22 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:11:38 -0400
Subject: [PATCH 08/30] fix 1.24.4

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

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index b1b03dac3..630cc1a6c 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -44,7 +44,7 @@ jobs:
            - python-version: '3.13'
              numpy-version: '1.23.5'
            - python-version: '3.13'
-             numpy-version: '1.24.1'
+             numpy-version: '1.24.4'
            - python-version: '3.13'
              numpy-version: '1.25.1'
            - python-version: '3.13'

From 119e715b2b8d5202701faaec57a7d1787825ef6f Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:19:17 -0400
Subject: [PATCH 09/30] fix pyproject

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 716a1dd99..2d395ce78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ classifiers = [
 dependencies = [
     "packaging",
     "numpy>=1.22.4",
-    "quantities>=0.14.1,<0.16.1"
+    "quantities>=16.1"
 ]
 
 [project.urls]

From b27f88044f6ac8cadab65af97ca984a657c8b59c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:20:34 -0400
Subject: [PATCH 10/30] oops

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2d395ce78..45e85dbdc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ classifiers = [
 dependencies = [
     "packaging",
     "numpy>=1.22.4",
-    "quantities>=16.1"
+    "quantities>=0.16.1"
 ]
 
 [project.urls]

From c9113f6e6e93cd246dd625122004017710912e43 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:25:54 -0400
Subject: [PATCH 11/30] fail-fast false

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

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 630cc1a6c..62a7a8a70 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
-      fail-fast: true
+      fail-fast: false # change back before MERGE
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",

From 11d9d7242adf2f852fbf87e79a9fe57463309d8b Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 12:50:53 -0400
Subject: [PATCH 12/30] update io-test

---
 .github/workflows/core-test.yml | 4 +++-
 .github/workflows/io-test.yml   | 8 +++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 62a7a8a70..1d14e9d86 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -27,7 +27,7 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0',]
+        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2',]
         exclude:
            - python-version: '3.9'
              numpy-version: '2.1'
@@ -49,6 +49,8 @@ jobs:
              numpy-version: '1.25.1'
            - python-version: '3.13'
              numpy-version: '1.26.4'
+           - python-version: '3.13'
+             numpy-version: '2.0.2'
 
     steps:
         - name: Set up Python ${{ matrix.python-version }}
diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index c609cc540..129f8c3f7 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -18,7 +18,13 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.11.9']
+        python-version: ['3.9', '3.12']
+        numpy-version: ['1.26.4', '2.0.2']
+        exclude:
+          - python-version: '3.12'
+            numpy-version: '1.26.4'
+          - python-version: '3.9'
+            numpy-version: '2.0.2'
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

From 0160830332149030b239b99dd31920a503484b5d Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 14:24:49 -0400
Subject: [PATCH 13/30] spiketrain set due to new numpy string

---
 neo/core/spiketrain.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
index 20b318406..7a84df57c 100644
--- a/neo/core/spiketrain.py
+++ b/neo/core/spiketrain.py
@@ -975,7 +975,7 @@ def _merge_array_annotations(self, others, sorting=None):
 
         omitted_keys_other = [
             key
-            for key in np.unique([key for other in others for key in other.array_annotations])
+            for key in set([key for other in others for key in other.array_annotations])
             if key not in self.array_annotations
         ]
 

From 10605e3b788bc07d08f0b424b9431045d3232e84 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 17:59:55 -0400
Subject: [PATCH 14/30] fix the casting of times

---
 neo/test/coretest/test_spiketrain.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/neo/test/coretest/test_spiketrain.py b/neo/test/coretest/test_spiketrain.py
index 8e5af92a7..6636c173f 100644
--- a/neo/test/coretest/test_spiketrain.py
+++ b/neo/test/coretest/test_spiketrain.py
@@ -315,6 +315,7 @@ def test__create_from_quantity_array(self):
 
     def test__create_from_quantity_array_with_dtype(self):
         times = np.arange(10, dtype="f4") * pq.ms
+        times = times.astype(dtype="f4")
         t_start = 0.0 * pq.s
         t_stop = 12.0 * pq.ms
         train1 = SpikeTrain(times, t_start=t_start, t_stop=t_stop)
@@ -346,6 +347,10 @@ def test__create_from_quantity_array_no_start_stop_units(self):
 
     def test__create_from_quantity_array_no_start_stop_units_with_dtype(self):
         times = np.arange(10, dtype="f4") * pq.ms
+        # this step is required for NumPy 2.0 which now casts to float64 in the case either value/array
+        # is float64 even if not necessary
+        # https://numpy.org/devdocs/numpy_2_0_migration_guide.html
+        times = times.astype(dtype="f4")
         t_start = 0.0
         t_stop = 12.0
         train1 = SpikeTrain(times, t_start=t_start, t_stop=t_stop)
@@ -1147,7 +1152,7 @@ def test_merge_multiple(self):
         expected *= time_unit
         sorting = np.argsort(expected)
         expected = expected[sorting]
-        np.testing.assert_array_equal(result.times, expected)
+        np.testing.assert_array_equal(result.times.magnitude, expected.magnitude)
 
         # Make sure array annotations are merged correctly
         self.assertTrue("label" not in result.array_annotations)

From 559b7397c389a812b0d34a800e9848f75acb4d0c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:07:42 -0400
Subject: [PATCH 15/30] more tests for core

---
 .github/workflows/core-test.yml      | 2 +-
 .github/workflows/io-test.yml        | 7 +------
 neo/test/coretest/test_spiketrain.py | 3 +++
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 1d14e9d86..1db158fc1 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -27,7 +27,7 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2',]
+        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1']
         exclude:
            - python-version: '3.9'
              numpy-version: '2.1'
diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 129f8c3f7..5a4259a2a 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,12 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
-        numpy-version: ['1.26.4', '2.0.2']
-        exclude:
-          - python-version: '3.12'
-            numpy-version: '1.26.4'
-          - python-version: '3.9'
-            numpy-version: '2.0.2'
+        numpy-version: ['1.26.4',]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
diff --git a/neo/test/coretest/test_spiketrain.py b/neo/test/coretest/test_spiketrain.py
index 6636c173f..3b63973af 100644
--- a/neo/test/coretest/test_spiketrain.py
+++ b/neo/test/coretest/test_spiketrain.py
@@ -315,6 +315,9 @@ def test__create_from_quantity_array(self):
 
     def test__create_from_quantity_array_with_dtype(self):
         times = np.arange(10, dtype="f4") * pq.ms
+        # this step is required for NumPy 2.0 which now casts to float64 in the case either value/array
+        # is float64 even if not necessary
+        # https://numpy.org/devdocs/numpy_2_0_migration_guide.html
         times = times.astype(dtype="f4")
         t_start = 0.0 * pq.s
         t_stop = 12.0 * pq.ms

From 34771c7ec91d114eab6f305137391588acafe624 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:14:08 -0400
Subject: [PATCH 16/30] try another action trick

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 5a4259a2a..e84e36b29 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
-        numpy-version: ['1.26.4',]
+        numpy-version: '1.26.4'
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

From 08d9a2eaef266dba3d11f906aeca298e1a41c093 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:22:37 -0400
Subject: [PATCH 17/30] fix matrix call

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index e84e36b29..41915ee74 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
-        numpy-version: '1.26.4'
+        numpy-version: ['1.26.4']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

From 18cf5ea09827537ec05134c8b37128f47dd197d8 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:28:46 -0400
Subject: [PATCH 18/30] try limiting to 1.26.4 during install

---
 .github/workflows/io-test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 41915ee74..6d98911d9 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,7 +19,6 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
-        numpy-version: ['1.26.4']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -91,9 +90,11 @@ jobs:
       - name: Install neo including dependencies
         # installation with dependencies is only required if no cache was found
         # restore-key hits should result in `cache-hit` == 'false'
+        # in the run we limit numpy for now. Change this in the next phase of numpy 2.0 support.
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
           pip install --upgrade -e .
+          pip install numpy==1.26.4
           pip install .[test]
 
       - name: Install neo without dependencies

From f36daa817fc4a751b68e3bbf293f8ededb1130d1 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:31:16 -0400
Subject: [PATCH 19/30] last attempt to get action working

---
 .github/workflows/io-test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 6d98911d9..a09a22655 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -90,11 +90,11 @@ jobs:
       - name: Install neo including dependencies
         # installation with dependencies is only required if no cache was found
         # restore-key hits should result in `cache-hit` == 'false'
-        # in the run we limit numpy for now. Change this in the next phase of numpy 2.0 support.
+        # in the run we don't do upgrade to prevent forced numpy 2.0. when ready
+        # change to pip install --upgrade -e . instead.
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          pip install --upgrade -e .
-          pip install numpy==1.26.4
+          pip install -e .
           pip install .[test]
 
       - name: Install neo without dependencies

From 8e6c3d497dbac861ed99bf5d75ca0cf31591b4bb Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:35:58 -0400
Subject: [PATCH 20/30] add numpy version there.

---
 .github/workflows/io-test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index a09a22655..291f85551 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,6 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
+        numpy-version: ["1.26.4"]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

From b67684b7ab8257b236ef8193d18c2875056f8163 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Thu, 17 Oct 2024 18:39:46 -0400
Subject: [PATCH 21/30] try the .yml env file

---
 environment_testing.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/environment_testing.yml b/environment_testing.yml
index 8ff8bd984..64488e835 100644
--- a/environment_testing.yml
+++ b/environment_testing.yml
@@ -4,3 +4,6 @@ channels:
 dependencies:
   - datalad
   - pip
+  # temporary have this here for IO testing while we decide how to deal with
+  # external packages not 2.0 ready
+  - numpy=1.26.4

From 7154a187f56804618a77f1d7bf55e479694d4166 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 06:02:25 -0400
Subject: [PATCH 22/30] another attempt to get numpy to work.

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 291f85551..688ddea51 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -96,6 +96,8 @@ jobs:
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
           pip install -e .
+          pip uninstall numpy
+          pip install numpy==1.26.4
           pip install .[test]
 
       - name: Install neo without dependencies

From 8df5dae60e92156c73cb394ec1aa98ecc8d0525c Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 06:08:13 -0400
Subject: [PATCH 23/30] add -y

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 688ddea51..50384fa46 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -96,8 +96,8 @@ jobs:
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
           pip install -e .
-          pip uninstall numpy
-          pip install numpy==1.26.4
+          pip uninstall numpy -y
+          pip install numpy==1.26.4 -y
           pip install .[test]
 
       - name: Install neo without dependencies

From d360787d9522fa145a84a61042359e7027a90f23 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 06:13:26 -0400
Subject: [PATCH 24/30] remove - y

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 50384fa46..4a487ee3f 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -97,7 +97,7 @@ jobs:
         run: |
           pip install -e .
           pip uninstall numpy -y
-          pip install numpy==1.26.4 -y
+          pip install numpy==1.26.4
           pip install .[test]
 
       - name: Install neo without dependencies

From 12cdec9143835ae7661702dbaa281ddb41eb926e Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 07:12:59 -0400
Subject: [PATCH 25/30] try not to download dhn_med_py

---
 .github/workflows/io-test.yml | 7 +------
 pyproject.toml                | 4 ++--
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 4a487ee3f..24e9f478b 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -19,7 +19,6 @@ jobs:
       fail-fast: true
       matrix:
         python-version: ['3.9', '3.12']
-        numpy-version: ["1.26.4"]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -91,13 +90,9 @@ jobs:
       - name: Install neo including dependencies
         # installation with dependencies is only required if no cache was found
         # restore-key hits should result in `cache-hit` == 'false'
-        # in the run we don't do upgrade to prevent forced numpy 2.0. when ready
-        # change to pip install --upgrade -e . instead.
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          pip install -e .
-          pip uninstall numpy -y
-          pip install numpy==1.26.4
+          pip install --upgrade -e .
           pip install .[test]
 
       - name: Install neo without dependencies
diff --git a/pyproject.toml b/pyproject.toml
index 45e85dbdc..170bfcc8b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,7 +45,7 @@ iocache = [
 ]
 
 test = [
-    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
+    # "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "pytest",
     "pytest-cov",
     # datalad   # this dependency is covered by conda (environment_testing.yml)
@@ -106,7 +106,7 @@ plexon2 = ["zugbruecke>=0.2; sys_platform!='win32'", "wenv; sys_platform!='win32
 all = [
     "coverage",
     "coveralls",
-    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
+    # "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "h5py",
     "igor2",
     "ipython",

From b6d6bb85ea51694e29db806510d7836bd9477a38 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 08:47:36 -0400
Subject: [PATCH 26/30] update action version number

---
 .github/workflows/core-test.yml | 6 +++---
 .github/workflows/io-test.yml   | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/core-test.yml b/.github/workflows/core-test.yml
index 1db158fc1..e19634ba8 100644
--- a/.github/workflows/core-test.yml
+++ b/.github/workflows/core-test.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
-      fail-fast: false # change back before MERGE
+      fail-fast: true
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
@@ -54,12 +54,12 @@ jobs:
 
     steps:
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Checkout repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
 
         - name: Install numpy ${{ matrix.numpy-version }}
           run: |
diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 24e9f478b..69b6ed98b 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -26,7 +26,7 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get current year-month
         id: date
@@ -38,7 +38,7 @@ jobs:
         run: |
           echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v3
+      - uses: actions/cache/restore@v4
         # Loading cache of ephys_testing_dataset
         id: cache-datasets
         with:
@@ -46,7 +46,7 @@ jobs:
           key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
           restore-keys: ${{ runner.os }}-datasets-
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: neo-test-env
           python-version: "${{ matrix.python-version }}"

From a3b753bd25903e2825be53544530bb2b496acb33 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 08:49:38 -0400
Subject: [PATCH 27/30] don't update miniconda version

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

diff --git a/.github/workflows/io-test.yml b/.github/workflows/io-test.yml
index 69b6ed98b..e5e0cd3a5 100644
--- a/.github/workflows/io-test.yml
+++ b/.github/workflows/io-test.yml
@@ -46,7 +46,7 @@ jobs:
           key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }}
           restore-keys: ${{ runner.os }}-datasets-
 
-      - uses: conda-incubator/setup-miniconda@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: neo-test-env
           python-version: "${{ matrix.python-version }}"

From f4545c2e059a0ba3bfcca471a13a592b9019701c Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 09:56:43 -0400
Subject: [PATCH 28/30] update rtd yaml

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 211f42ae3..0f3efcc66 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 sphinx:
    configuration: doc/source/conf.py

From 4b0fc8ecf99c51a9ca2be81eec36c6a475e4ad26 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 18 Oct 2024 10:21:28 -0400
Subject: [PATCH 29/30] revert to 3.11, errors with 3.12

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 0f3efcc66..211f42ae3 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.11"
 
 sphinx:
    configuration: doc/source/conf.py

From d8edd683efc9ed0de330f4b2100898f5e59b086e Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Mon, 21 Oct 2024 10:12:04 -0400
Subject: [PATCH 30/30] fix pyproject after release

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 65e276ebe..04c6f1c3c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ version = "0.13.4"
 authors = [{name = "Neo authors and contributors"}]
 description = "Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats"
 readme = "README.rst"
-requires-python = ">=3.9,<3.13" # 3.13 will require NumPy > 2.0 (Windows issue in CI)
+requires-python = ">=3.9"
 license = {text = "BSD 3-Clause License"}
 classifiers = [
     "Development Status :: 4 - Beta",