From 49dddeb6c21d18c2216316194dd4d81b2bf46838 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:21:57 +0200
Subject: [PATCH 01/11] check that build action can use TMPDIR Fixes #52

---
 tests/test_container_template.py | 34 +++++++++++++++++++++++++++++---
 1 file changed, 31 insertions(+), 3 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index aab0bb7..22b2a34 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -11,6 +11,7 @@
 import os
 import socket
 import subprocess
+import tempfile
 
 
 # port used by tests
@@ -18,17 +19,27 @@
 sock.bind(('', 0))
 port = sock.getsockname()[1]
 
-# Check that (1) singularity exist, and (2) if not, check for docker.
+# Check that (1) singularity or apptainer executables exist, 
+# and (2) if not, check for docker.
 # If neither are found, tests will fall back to plain python.
+# This may be useful for testing on a local machine, but should 
+# be revised for the particular usecase.
 try:
     pth = os.path.join('containers', 'container_template.sif')
-    out = subprocess.run('singularity')
+    try:
+        out = subprocess.run('singularity', check=False)
+    except FileNotFoundError:
+        try:
+            out = subprocess.run('apptainer', check=False)
+        except FileNotFoundError as exc:
+            raise FileNotFoundError from exc
     cwd = os.getcwd()
     PREFIX = f'singularity run {pth} python'
     PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
+    PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + '{custom_mount}' + f'{pth} python'
 except FileNotFoundError:
     try:
-        out = subprocess.run('docker')
+        out = subprocess.run('docker', check=False)
         pwd = os.getcwd()
         PREFIX = (f'docker run -p {port}:{port} ' +
                   'ghcr.io/precimed/container_template python')
@@ -36,6 +47,11 @@
             f'docker run -p {port}:{port} ' +
             f'--mount type=bind,source={pwd},target={pwd} ' +
             'ghcr.io/precimed/container_template python')
+        PREFIX_CUSTOM_MOUNT = (
+            f'docker run -p {port}:{port} ' +
+            f'--mount type=bind,source={pwd},target={pwd} ' +
+            '{custom_mount} ' +
+            'ghcr.io/precimed/container_template python')
     except FileNotFoundError:
         # neither singularity nor docker found, fall back to plain python
         PREFIX = 'python'
@@ -62,6 +78,17 @@ def test_container_template_python_script():
     assert out.returncode == 0
 
 
+def test_container_template_python_script_from_tempdir():
+    '''test that the tempdir is working'''
+    with tempfile.TemporaryDirectory() as d:
+        os.system(f'cp {pwd}/tests/extras/hello.py {d}/')
+        custom_mount = f'--mount type=bind,source={d},target=/temp/'
+        call = f'{PREFIX_CUSTOM_MOUNT.format(custom_mount=custom_mount)} ' + \
+            '/temp/hello.py'
+        out = subprocess.run(call.split(' '), check=False)
+        assert out.returncode == 0
+
+
 def test_container_template_python_packages():
     '''test that the Python packages are installed'''
     packages = [
@@ -78,3 +105,4 @@ def test_container_template_python_packages():
     call = f"{PREFIX} -c '{importstr}'"
     out = subprocess.run(call, shell=True)
     assert out.returncode == 0
+

From 6d5306ec6f20dc70921817815198d4b454ba3bc7 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:24:56 +0200
Subject: [PATCH 02/11] flake8 must be happy

---
 tests/test_container_template.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 22b2a34..4244390 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -19,10 +19,10 @@
 sock.bind(('', 0))
 port = sock.getsockname()[1]
 
-# Check that (1) singularity or apptainer executables exist, 
+# Check that (1) singularity or apptainer executables exist,
 # and (2) if not, check for docker.
 # If neither are found, tests will fall back to plain python.
-# This may be useful for testing on a local machine, but should 
+# This may be useful for testing on a local machine, but should
 # be revised for the particular usecase.
 try:
     pth = os.path.join('containers', 'container_template.sif')
@@ -36,7 +36,8 @@
     cwd = os.getcwd()
     PREFIX = f'singularity run {pth} python'
     PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
-    PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + '{custom_mount}' + f'{pth} python'
+    PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + \
+        '{custom_mount}' + f'{pth} python'
 except FileNotFoundError:
     try:
         out = subprocess.run('docker', check=False)
@@ -105,4 +106,3 @@ def test_container_template_python_packages():
     call = f"{PREFIX} -c '{importstr}'"
     out = subprocess.run(call, shell=True)
     assert out.returncode == 0
-

From 7bf75e5190dc1cb9143a9584cd19c9909e574c9c Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:26:10 +0200
Subject: [PATCH 03/11] PREFIX_CUSTOM_MOUNT defined

---
 tests/test_container_template.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 4244390..3766f53 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -57,6 +57,7 @@
         # neither singularity nor docker found, fall back to plain python
         PREFIX = 'python'
         PREFIX_MOUNT = 'python'
+        PREFIX_CUSTOM_MOUNT = 'python'
 
 
 def test_assert():

From ce496b9cdcc45eaef9819931c7b84ce5912daf60 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 14:27:47 +0200
Subject: [PATCH 04/11] pwd to cwd

---
 tests/test_container_template.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 3766f53..5574ab6 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -41,16 +41,16 @@
 except FileNotFoundError:
     try:
         out = subprocess.run('docker', check=False)
-        pwd = os.getcwd()
+        cwd = os.getcwd()
         PREFIX = (f'docker run -p {port}:{port} ' +
                   'ghcr.io/precimed/container_template python')
         PREFIX_MOUNT = (
             f'docker run -p {port}:{port} ' +
-            f'--mount type=bind,source={pwd},target={pwd} ' +
+            f'--mount type=bind,source={cwd},target={cwd} ' +
             'ghcr.io/precimed/container_template python')
         PREFIX_CUSTOM_MOUNT = (
             f'docker run -p {port}:{port} ' +
-            f'--mount type=bind,source={pwd},target={pwd} ' +
+            f'--mount type=bind,source={cwd},target={cwd} ' +
             '{custom_mount} ' +
             'ghcr.io/precimed/container_template python')
     except FileNotFoundError:
@@ -74,8 +74,8 @@ def test_container_template_python():
 
 def test_container_template_python_script():
     '''test that Python can run a script'''
-    pwd = os.getcwd() if PREFIX.rfind('docker') >= 0 else '.'
-    call = f'''{PREFIX_MOUNT} {pwd}/tests/extras/hello.py'''
+    cwd = os.getcwd() if PREFIX.rfind('docker') >= 0 else '.'
+    call = f'''{PREFIX_MOUNT} {cwd}/tests/extras/hello.py'''
     out = subprocess.run(call.split(' '), capture_output=True)
     assert out.returncode == 0
 
@@ -83,7 +83,7 @@ def test_container_template_python_script():
 def test_container_template_python_script_from_tempdir():
     '''test that the tempdir is working'''
     with tempfile.TemporaryDirectory() as d:
-        os.system(f'cp {pwd}/tests/extras/hello.py {d}/')
+        os.system(f'cp {cwd}/tests/extras/hello.py {d}/')
         custom_mount = f'--mount type=bind,source={d},target=/temp/'
         call = f'{PREFIX_CUSTOM_MOUNT.format(custom_mount=custom_mount)} ' + \
             '/temp/hello.py'

From ede9c732c5949330d06ed3e39c444c209117bc65 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:24:33 +0200
Subject: [PATCH 05/11] cwd

---
 tests/test_container_template.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 5574ab6..2fc3326 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -24,6 +24,7 @@
 # If neither are found, tests will fall back to plain python.
 # This may be useful for testing on a local machine, but should
 # be revised for the particular usecase.
+cwd = os.getcwd()
 try:
     pth = os.path.join('containers', 'container_template.sif')
     try:
@@ -33,7 +34,6 @@
             out = subprocess.run('apptainer', check=False)
         except FileNotFoundError as exc:
             raise FileNotFoundError from exc
-    cwd = os.getcwd()
     PREFIX = f'singularity run {pth} python'
     PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
     PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + \
@@ -41,7 +41,6 @@
 except FileNotFoundError:
     try:
         out = subprocess.run('docker', check=False)
-        cwd = os.getcwd()
         PREFIX = (f'docker run -p {port}:{port} ' +
                   'ghcr.io/precimed/container_template python')
         PREFIX_MOUNT = (

From f607580ec5190f7aead8c20653f0c578f4c08258 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:41:50 +0200
Subject: [PATCH 06/11] should work

---
 tests/test_container_template.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 2fc3326..d68c15a 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -83,10 +83,10 @@ def test_container_template_python_script_from_tempdir():
     '''test that the tempdir is working'''
     with tempfile.TemporaryDirectory() as d:
         os.system(f'cp {cwd}/tests/extras/hello.py {d}/')
-        custom_mount = f'--mount type=bind,source={d},target=/temp/'
+        custom_mount = f'--mount type=bind,source={d},target={d}'
         call = f'{PREFIX_CUSTOM_MOUNT.format(custom_mount=custom_mount)} ' + \
-            '/temp/hello.py'
-        out = subprocess.run(call.split(' '), check=False)
+            f'{d}/hello.py'
+        out = subprocess.run(call, shell=True, check=False)
         assert out.returncode == 0
 
 

From 1df34337c51955b0375c6dbcfd939e86bc418a68 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:06:14 +0000
Subject: [PATCH 07/11] revise tests for apptainer runtime

---
 tests/test_container_template.py | 31 ++++++++++++++++++++-----------
 1 file changed, 20 insertions(+), 11 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index d68c15a..425d0a5 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -28,32 +28,36 @@
 try:
     pth = os.path.join('containers', 'container_template.sif')
     try:
-        out = subprocess.run('singularity', check=False)
+        runtime = 'apptainer'
+        out = subprocess.run(runtime, check=False)
     except FileNotFoundError:
         try:
-            out = subprocess.run('apptainer', check=False)
+            runtime = 'singularity'
+            out = subprocess.run(runtime, check=False)
         except FileNotFoundError as exc:
             raise FileNotFoundError from exc
-    PREFIX = f'singularity run {pth} python'
-    PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
-    PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + \
+    PREFIX = f'{runtime} run {pth} python'
+    PREFIX_MOUNT = f'{runtime} run --home={cwd}:/home/ {pth} python'
+    PREFIX_CUSTOM_MOUNT = f'{runtime} run --home={cwd}:/home/ ' + \
         '{custom_mount}' + f'{pth} python'
 except FileNotFoundError:
     try:
-        out = subprocess.run('docker', check=False)
-        PREFIX = (f'docker run -p {port}:{port} ' +
+        runtime = 'docker'
+        out = subprocess.run(runtime, check=False)
+        PREFIX = (f'{runtime} run -p {port}:{port} ' +
                   'ghcr.io/precimed/container_template python')
         PREFIX_MOUNT = (
-            f'docker run -p {port}:{port} ' +
+            f'{runtime} run -p {port}:{port} ' +
             f'--mount type=bind,source={cwd},target={cwd} ' +
             'ghcr.io/precimed/container_template python')
         PREFIX_CUSTOM_MOUNT = (
-            f'docker run -p {port}:{port} ' +
+            f'{runtime} run -p {port}:{port} ' +
             f'--mount type=bind,source={cwd},target={cwd} ' +
             '{custom_mount} ' +
             'ghcr.io/precimed/container_template python')
     except FileNotFoundError:
         # neither singularity nor docker found, fall back to plain python
+        runtime = None
         PREFIX = 'python'
         PREFIX_MOUNT = 'python'
         PREFIX_CUSTOM_MOUNT = 'python'
@@ -73,7 +77,7 @@ def test_container_template_python():
 
 def test_container_template_python_script():
     '''test that Python can run a script'''
-    cwd = os.getcwd() if PREFIX.rfind('docker') >= 0 else '.'
+    cwd = os.getcwd() if runtime == 'docker' >= 0 else '.'
     call = f'''{PREFIX_MOUNT} {cwd}/tests/extras/hello.py'''
     out = subprocess.run(call.split(' '), capture_output=True)
     assert out.returncode == 0
@@ -83,7 +87,12 @@ def test_container_template_python_script_from_tempdir():
     '''test that the tempdir is working'''
     with tempfile.TemporaryDirectory() as d:
         os.system(f'cp {cwd}/tests/extras/hello.py {d}/')
-        custom_mount = f'--mount type=bind,source={d},target={d}'
+        if runtime == 'docker':
+            custom_mount = f'--mount type=bind,source={d},target={d}'
+        elif runtime in ['apptainer', 'singularity']:
+            custom_mount = f'--bind {d}:{d} '
+        else:
+            custom_mount = ''
         call = f'{PREFIX_CUSTOM_MOUNT.format(custom_mount=custom_mount)} ' + \
             f'{d}/hello.py'
         out = subprocess.run(call, shell=True, check=False)

From 63d7d1b7e7e45eaaa85cd88107347df305aef09a Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 17:07:32 +0200
Subject: [PATCH 08/11] bah

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

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 425d0a5..3f37b31 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -77,7 +77,7 @@ def test_container_template_python():
 
 def test_container_template_python_script():
     '''test that Python can run a script'''
-    cwd = os.getcwd() if runtime == 'docker' >= 0 else '.'
+    cwd = os.getcwd() if runtime == 'docker' else '.'
     call = f'''{PREFIX_MOUNT} {cwd}/tests/extras/hello.py'''
     out = subprocess.run(call.split(' '), capture_output=True)
     assert out.returncode == 0

From 43a262c17a92756c7fb33656500d151232e0f200 Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 17:10:42 +0200
Subject: [PATCH 09/11] test using py.test inner and outer scope

---
 .github/workflows/container_build.yml | 13 +++++++++----
 test-requirements.txt                 |  1 +
 2 files changed, 10 insertions(+), 4 deletions(-)
 create mode 100644 test-requirements.txt

diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
index 5c141da..db56b62 100644
--- a/.github/workflows/container_build.yml
+++ b/.github/workflows/container_build.yml
@@ -10,7 +10,7 @@ on:
     tags:
       - "v*.*.*"
 env:
-  TEST_TAG: ghcr.io/precimed/container_template:test
+  LATEST_TAG: ghcr.io/precimed/container_template:latest
 
 jobs:
   docker:
@@ -51,13 +51,18 @@ jobs:
         with:
           context: "{{defaultContext}}:docker"
           load: true
-          tags: ${{ env.TEST_TAG }}
+          tags: ${{ env.LATEST_TAG }}
           file:
             ./dockerfiles/container_template/Dockerfile
 
-      - name: Run unit tests
+      - name: Run unit tests I
         run: |
-          docker run --rm -v ${{ github.workspace }}:/home ${{ env.TEST_TAG }} py.test -v tests
+          docker run --rm -v ${{ github.workspace }}:/home ${{ env.LATEST_TAG }} py.test -v tests
+      
+      - name: Run unit tests II
+        run: |
+          pip install -r test-requirements.txt
+          py.test -v tests
 
       - name: Build
         uses: docker/build-push-action@v6
diff --git a/test-requirements.txt b/test-requirements.txt
new file mode 100644
index 0000000..e079f8a
--- /dev/null
+++ b/test-requirements.txt
@@ -0,0 +1 @@
+pytest

From dfbbcd290c7821390ba6cb7777aadf5cbf1358bd Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 21:24:51 +0200
Subject: [PATCH 10/11] don't assing docker port

---
 tests/test_container_template.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/tests/test_container_template.py b/tests/test_container_template.py
index 3f37b31..1e50208 100644
--- a/tests/test_container_template.py
+++ b/tests/test_container_template.py
@@ -9,16 +9,10 @@
 """
 
 import os
-import socket
 import subprocess
 import tempfile
 
 
-# port used by tests
-sock = socket.socket()
-sock.bind(('', 0))
-port = sock.getsockname()[1]
-
 # Check that (1) singularity or apptainer executables exist,
 # and (2) if not, check for docker.
 # If neither are found, tests will fall back to plain python.
@@ -44,14 +38,14 @@
     try:
         runtime = 'docker'
         out = subprocess.run(runtime, check=False)
-        PREFIX = (f'{runtime} run -p {port}:{port} ' +
+        PREFIX = (f'{runtime} run ' +
                   'ghcr.io/precimed/container_template python')
         PREFIX_MOUNT = (
-            f'{runtime} run -p {port}:{port} ' +
+            f'{runtime} run ' +
             f'--mount type=bind,source={cwd},target={cwd} ' +
             'ghcr.io/precimed/container_template python')
         PREFIX_CUSTOM_MOUNT = (
-            f'{runtime} run -p {port}:{port} ' +
+            f'{runtime} run ' +
             f'--mount type=bind,source={cwd},target={cwd} ' +
             '{custom_mount} ' +
             'ghcr.io/precimed/container_template python')

From dc89260c832c1a4511911fcd2715fbe70536ff4d Mon Sep 17 00:00:00 2001
From: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date: Wed, 2 Oct 2024 21:34:11 +0200
Subject: [PATCH 11/11] squash some pytest warnings

---
 tests/pytest.ini | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 tests/pytest.ini

diff --git a/tests/pytest.ini b/tests/pytest.ini
new file mode 100644
index 0000000..8f2ad61
--- /dev/null
+++ b/tests/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+cache_dir = /tmp/pytest-cache/
\ No newline at end of file