Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
sagar87 merged 11 commits into from
Jan 29, 2023
Merged

Plotting MVP #3

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
aaca115
Harald's code within org
timtreis Jan 28, 2023
3417005
got tests running
timtreis Jan 28, 2023
9d54e99
Updated toml to mirror spatialdata for testing
timtreis Jan 28, 2023
42499f7
Tried fixing toml
timtreis Jan 28, 2023
3b96a92
Copied test.yaml from spatialdata
timtreis Jan 28, 2023
49647ef
added spatialdata to toml
timtreis Jan 28, 2023
20134c0
Removed dummy test
timtreis Jan 28, 2023
a195aef
added matplotlib to toml
timtreis Jan 28, 2023
9322ee9
changed tests so that BOTH 3.9 and 3.10 (hopefully) pass
timtreis Jan 28, 2023
e70149c
Implemented basic table subsetting
timtreis Jan 28, 2023
a2f03b2
Added negative tests to get_images()
timtreis Jan 28, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 9 additions & 9 deletions .github/workflows/test.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python: ["3.8", "3.10"]
python: ["3.9", "3.10"]
os: [ubuntu-latest]

env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
- name: Install test dependencies
run: |
python -m pip install --upgrade pip wheel
pip install codecov
pip install pytest-cov
- name: Install dependencies
run: |
pip install ".[dev,test]"
pip install -e ".[dev,test]"
- name: Test
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
run: |
pytest -v --cov --color=yes
- name: Upload coverage
env:
CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
pytest -v --cov --color=yes --cov-report=xml
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
name: coverage
verbose: true
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down
54 changes: 31 additions & 23 deletions pyproject.toml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
{name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
"anndata",
# for debug logging (referenced from the issue template)
"session-info"
"numpy",
"xarray",
"zarr",
# "ome_zarr",
"ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
"spatialdata@git+https://github.com/scverse/spatialdata",
"spatial_image",
"multiscale_spatial_image",
"xarray-schema",
"pygeos",
"matplotlib",
"geopandas",
"shapely==2.0rc2",
"pyarrow",
"rich",
"tqdm",
"typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
# CLI for bumping the version number
# dev version generation
"bump2version",
"pre-commit",
"twine>=4.0.2"
]
doc = [
"sphinx>=4",
"sphinx>=4.5",
"sphinx-book-theme>=0.3.3",
"myst-nb",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
# For notebooks
"ipykernel",
"ipython",
"ipython>=8.6.0",
"sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
"**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
"--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
# "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Plotting MVP#3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

sagar87
merged 11 commits into

from

Jan 29, 2023
 Merged


Plotting MVP
#3
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


11 commits


Select commit
Hold shift + click to select a range
aaca115

Harald's code within org


timtreis Jan 28, 2023
3417005

got tests running


timtreis Jan 28, 2023
9d54e99

Updated toml to mirror spatialdata for testing


timtreis Jan 28, 2023
42499f7

Tried fixing toml


timtreis Jan 28, 2023
3b96a92

Copied test.yaml from spatialdata


timtreis Jan 28, 2023
49647ef

added spatialdata to toml


timtreis Jan 28, 2023
20134c0

Removed dummy test


timtreis Jan 28, 2023
a195aef

added matplotlib to toml


timtreis Jan 28, 2023
9322ee9

changed tests so that BOTH 3.9 and 3.10 (hopefully) pass


timtreis Jan 28, 2023
e70149c

Implemented basic table subsetting


timtreis Jan 28, 2023
a2f03b2

Added negative tests to get_images()


timtreis Jan 28, 2023

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


18 changes: 9 additions & 9 deletions
.github/workflows/test.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ jobs:
 strategy:
 fail-fast: false
 matrix:
 python: ["3.8", "3.10"]
 python: ["3.9", "3.10"]
 os: [ubuntu-latest]

 env:
Expand DownExpand Up@@ -44,19 +44,19 @@ jobs:
 - name: Install test dependencies
 run: |
 python -m pip install --upgrade pip wheel
 pip install codecov
 pip install pytest-cov
 - name: Install dependencies
 run: |
 pip install ".[dev,test]"
 pip install -e ".[dev,test]"
 - name: Test
 env:
 MPLBACKEND: agg
 PLATFORM: ${{ matrix.os }}
 DISPLAY: :42
 run: |
 pytest -v --cov --color=yes
 - name: Upload coverage
env:
 CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --required --flags=unittests
 pytest -v --cov --color=yes --cov-report=xml
 - name: Upload coverage to Codecov
uses: codecov/codecov-action@v3.1.1
with:
 name: coverage
verbose: true

2 changes: 1 addition & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
[link-tests]: https://github.com/scverse/spatialdata-plot/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/spatialdata-plot

doc -> https://docs.google.com/document/d/1fNYJV88gBLKnshIWkATn4pxgUsgPI0UNwWe7KGVkiEo/edit
A very interesting piece of code

## Getting started

Expand Down

54 changes: 31 additions & 23 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,9 +6,9 @@ requires = ["hatchling"]
[project]
name = "spatialdata-plot"
version = "0.0.1"
description = "A very interesting piece of code"
description = "Static plotting for spatialdata."
readme = "README.md"
requires-python = ">=3.8"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
 {name = "scverse"},
Expand All@@ -21,26 +21,38 @@ urls.Source = "https://github.com/scverse/spatialdata-plot"
urls.Home-page = "https://github.com/scverse/spatialdata-plot"
dependencies = [
 "anndata",
 # for debug logging (referenced from the issue template)
 "session-info"
 "numpy",
 "xarray",
 "zarr",
# "ome_zarr",
 "ome_zarr@git+https://github.com/LucaMarconato/ome-zarr-py@bug_fix_io",
 "spatialdata@git+https://github.com/scverse/spatialdata",
 "spatial_image",
 "multiscale_spatial_image",
 "xarray-schema",
 "pygeos",
 "matplotlib",
 "geopandas",
 "shapely==2.0rc2",
 "pyarrow",
 "rich",
 "tqdm",
 "typing_extensions>=4.0.0",
]

[project.optional-dependencies]
dev = [
 # CLI for bumping the version number
 # dev version generation
 "bump2version",
 "pre-commit",
 "twine>=4.0.2"
]
doc = [
 "sphinx>=4",
 "sphinx>=4.5",
 "sphinx-book-theme>=0.3.3",
 "myst-nb",
 "sphinxcontrib-bibtex>=1.0.0",
 "sphinx-autodoc-typehints",
 # For notebooks
 "ipykernel",
 "ipython",
 "ipython>=8.6.0",
 "sphinx-copybutton",
]
test = [
Expand All@@ -49,7 +61,7 @@ test = [
]

[tool.coverage.run]
source = ["spatialdata_plot"]
source = ["spatialdata"]
omit = [
 "**/test_*.py",
]
Expand All@@ -58,8 +70,13 @@ omit = [
testpaths = ["tests"]
xfail_strict = true
addopts = [
# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
 "--import-mode=importlib", # allow using test files with same name
]
# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
filterwarnings = [
 # "ignore:.*U.*mode is deprecated:DeprecationWarning",
]

[tool.isort]
include_trailing_comma = true
Expand All@@ -69,7 +86,7 @@ skip_glob = ["docs/*"]

[tool.black]
line-length = 120
target-version = ['py38']
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
Expand All@@ -91,14 +108,5 @@ exclude = '''
[tool.jupytext]
formats = "ipynb,md"

[tool.cruft]
skip = [
 "tests",
 "src/**/__init__.py",
 "src/**/basic.py",
 "docs/api.md",
 "docs/changelog.md",
 "docs/references.bib",
 "docs/references.md",
 "docs/notebooks/example.ipynb"
]
[tool.hatch.metadata]
allow-direct-references = true
Loading