MultiMM 2.1.0__tar.gz → 2.1.1__tar.gz

{multimm-2.1.0/src/MultiMM.egg-info → multimm-2.1.1}/PKG-INFO

@@ -1,9 +1,14 @@
 Metadata-Version: 2.4
 Name: MultiMM
-Version: 2.1.0
+Version: 2.1.1
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Author-email: Sebastian Korsak <s.korsak@datascience.edu.pl>
 License: GNU General Public License v3.0
+Project-URL: Homepage, https://github.com/SFGLab/MultiMM
+Project-URL: Documentation, https://sfglab.github.io/MultiMM/
+Project-URL: Source, https://github.com/SFGLab/MultiMM
+Project-URL: Issues, https://github.com/SFGLab/MultiMM/issues
+Project-URL: Changelog, https://github.com/SFGLab/MultiMM/releases
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: POSIX :: Linux
@@ -39,13 +44,15 @@ Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 <p align="center">
-  <img src="docs/assets/multimm_logo.svg" alt="MultiMM" width="100%">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/multimm_logo.png" alt="MultiMM" width="100%">
 </p>
 
+[![PyPI](https://img.shields.io/pypi/v/MultiMM)](https://pypi.org/project/MultiMM/) · **[Documentation](https://sfglab.github.io/MultiMM/)** · [Source](https://github.com/SFGLab/MultiMM)
+
 **MultiMM** is an [OpenMM](https://openmm.org)-based tool for building 3D models of chromatin, from single genomic regions to the whole human genome. It is *multiscale*: one energy function covers nucleosomes, loops and TADs, A/B compartments, chromosome territories and the nucleus. You give it loop calls, and optionally compartments or a Hi-C map, and it returns a 3D structure that you can open in any molecular viewer. The model is fast because it starts from a compact Hilbert-curve conformation and runs on GPUs through OpenMM.
 
 <p align="center">
-  <img src="docs/assets/workflow.png" alt="MultiMM workflow" width="720">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/workflow.png" alt="MultiMM workflow" width="720">
 </p>
 
 ## Scales of modelling
@@ -109,7 +116,7 @@ OUT_PATH         = results/chr1_region
 
 ## Documentation
 
-The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](docs). To read it locally:
+The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](https://github.com/SFGLab/MultiMM/tree/main/docs). To read it locally:
 
 ```bash
 pip install mkdocs-material

{multimm-2.1.0 → multimm-2.1.1}/README.md

@@ -1,11 +1,13 @@
 <p align="center">
-  <img src="docs/assets/multimm_logo.svg" alt="MultiMM" width="100%">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/multimm_logo.png" alt="MultiMM" width="100%">
 </p>
 
+[![PyPI](https://img.shields.io/pypi/v/MultiMM)](https://pypi.org/project/MultiMM/) · **[Documentation](https://sfglab.github.io/MultiMM/)** · [Source](https://github.com/SFGLab/MultiMM)
+
 **MultiMM** is an [OpenMM](https://openmm.org)-based tool for building 3D models of chromatin, from single genomic regions to the whole human genome. It is *multiscale*: one energy function covers nucleosomes, loops and TADs, A/B compartments, chromosome territories and the nucleus. You give it loop calls, and optionally compartments or a Hi-C map, and it returns a 3D structure that you can open in any molecular viewer. The model is fast because it starts from a compact Hilbert-curve conformation and runs on GPUs through OpenMM.
 
 <p align="center">
-  <img src="docs/assets/workflow.png" alt="MultiMM workflow" width="720">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/workflow.png" alt="MultiMM workflow" width="720">
 </p>
 
 ## Scales of modelling
@@ -69,7 +71,7 @@ OUT_PATH         = results/chr1_region
 
 ## Documentation
 
-The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](docs). To read it locally:
+The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](https://github.com/SFGLab/MultiMM/tree/main/docs). To read it locally:
 
 ```bash
 pip install mkdocs-material

{multimm-2.1.0 → multimm-2.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MultiMM"
-version = "2.1.0"
+version = "2.1.1"
 description = "A tool for chromatin modeling from nucleosomes to chromosomal territories."
 readme = "README.md"
 authors = [
@@ -38,6 +38,13 @@ dependencies = [
     "scikit-image>=0.21.0",
 ]
 
+[project.urls]
+Homepage = "https://github.com/SFGLab/MultiMM"
+Documentation = "https://sfglab.github.io/MultiMM/"
+Source = "https://github.com/SFGLab/MultiMM"
+Issues = "https://github.com/SFGLab/MultiMM/issues"
+Changelog = "https://github.com/SFGLab/MultiMM/releases"
+
 [project.optional-dependencies]
 # .hic files need hic-straw, which compiles C++ code and may fail to install; .cool/.mcool do not need it
 hic = ["hic-straw>=1.3.1"]

{multimm-2.1.0 → multimm-2.1.1/src/MultiMM.egg-info}/PKG-INFO

@@ -1,9 +1,14 @@
 Metadata-Version: 2.4
 Name: MultiMM
-Version: 2.1.0
+Version: 2.1.1
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Author-email: Sebastian Korsak <s.korsak@datascience.edu.pl>
 License: GNU General Public License v3.0
+Project-URL: Homepage, https://github.com/SFGLab/MultiMM
+Project-URL: Documentation, https://sfglab.github.io/MultiMM/
+Project-URL: Source, https://github.com/SFGLab/MultiMM
+Project-URL: Issues, https://github.com/SFGLab/MultiMM/issues
+Project-URL: Changelog, https://github.com/SFGLab/MultiMM/releases
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: POSIX :: Linux
@@ -39,13 +44,15 @@ Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 <p align="center">
-  <img src="docs/assets/multimm_logo.svg" alt="MultiMM" width="100%">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/multimm_logo.png" alt="MultiMM" width="100%">
 </p>
 
+[![PyPI](https://img.shields.io/pypi/v/MultiMM)](https://pypi.org/project/MultiMM/) · **[Documentation](https://sfglab.github.io/MultiMM/)** · [Source](https://github.com/SFGLab/MultiMM)
+
 **MultiMM** is an [OpenMM](https://openmm.org)-based tool for building 3D models of chromatin, from single genomic regions to the whole human genome. It is *multiscale*: one energy function covers nucleosomes, loops and TADs, A/B compartments, chromosome territories and the nucleus. You give it loop calls, and optionally compartments or a Hi-C map, and it returns a 3D structure that you can open in any molecular viewer. The model is fast because it starts from a compact Hilbert-curve conformation and runs on GPUs through OpenMM.
 
 <p align="center">
-  <img src="docs/assets/workflow.png" alt="MultiMM workflow" width="720">
+  <img src="https://raw.githubusercontent.com/SFGLab/MultiMM/main/docs/assets/workflow.png" alt="MultiMM workflow" width="720">
 </p>
 
 ## Scales of modelling
@@ -109,7 +116,7 @@ OUT_PATH         = results/chr1_region
 
 ## Documentation
 
-The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](docs). To read it locally:
+The full documentation, with the mathematics of every force and a table of all arguments, is written with [MkDocs](https://www.mkdocs.org) and its source is in [`docs/`](https://github.com/SFGLab/MultiMM/tree/main/docs). To read it locally:
 
 ```bash
 pip install mkdocs-material

{multimm-2.1.0 → multimm-2.1.1}/src/multimm/__init__.py

@@ -8,4 +8,4 @@ def main(*args, **kwargs):
     return _main(*args, **kwargs)
 
 
-__version__ = "2.1.0"
+__version__ = "2.1.1"

{multimm-2.1.0 → multimm-2.1.1}/src/multimm/logger.py

@@ -697,10 +697,27 @@ def print_banner(version: Optional[str] = None) -> None:
 
     pad = "  " + (" " * (sym_w + 3) if show_sym else "")
     beads = "".join(gradient("●─" if i < 15 else "●", i / 15, i / 15) for i in range(16))
+
+    # one random chromatin fact right under the tagline, aligned with it
+    from .facts import random_fact
+
+    width = max(40, min(cols, 100) - len(pad) - 4)
+    wrapped = textwrap.wrap(random_fact(), width)
+    rule = "─" * min(width, 56)
+    quote = [pad + _tint("◆ did you know?  " + rule[:max(0, len(rule) - 17)], italic=True)]
+    for k, ln in enumerate(wrapped):
+        t0, t1 = k / len(wrapped), (k + 1) / len(wrapped)
+        mark = "❝ " if k == 0 else "  "
+        end = " ❞" if k == len(wrapped) - 1 else ""
+        quote.append(pad + _tint(mark + ln + end, t0, t1, italic=True))
+
     lines += [
         "",
         pad + gradient(" ┈ ".join(_SCALES)),
         pad + f"{d}multiscale modelling of chromatin{rst}" + (f"   {gradient('v' + version)}" if version else ""),
+        "",
+        *quote,
+        "",
         pad + beads,
         "",
         f"  {d}Creator{rst}      Sebastian Korsak  (Warsaw, Poland)",
@@ -708,19 +725,6 @@ def print_banner(version: Optional[str] = None) -> None:
         f"  {d}Contact{rst}      s.korsak@datascience.edu.pl · d.plewczynski@datascience.edu.pl",
         "",
     ]
-    # one random chromatin fact: gradient rule, italic gradient text, closing mark
-    from .facts import random_fact
-
-    width = max(40, min(cols, 100) - 10)
-    wrapped = textwrap.wrap(random_fact(), width)
-    rule = "─" * min(width + 2, 60)
-    lines.append("  " + _tint("◆ did you know?  " + rule[:max(0, len(rule) - 17)], italic=True))
-    for k, ln in enumerate(wrapped):
-        t0, t1 = k / len(wrapped), (k + 1) / len(wrapped)
-        mark = "❝ " if k == 0 else "  "
-        end = " ❞" if k == len(wrapped) - 1 else ""
-        lines.append("  " + _tint(mark + ln + end, t0, t1, italic=True))
-    lines.append("")
     for line in lines:
         _emit(line)
 
@@ -733,7 +737,7 @@ if __name__ == "__main__":
     v = int(sys.argv[1]) if len(sys.argv) > 1 else 0
     setup_logger(verbosity=v)
     log = logging.getLogger("multimm.demo")
-    print_banner("2.1.0")
+    print_banner("2.1.1")
     with stage("Input data", 3) as s:
         for name in ("Loops", "Compartments", "Hi-C"):
             s.next(name)