From a78b395948ba30f4322d1ff7026f22bb9d50889f Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 19 Dec 2023 19:41:44 -0600 Subject: [PATCH 1/9] bumped version --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index db2c903..60cf864 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -54,7 +54,7 @@ # needed to use forward annotations: https://docs.python.org/3/whatsnew/3.7.html#whatsnew37-pep563 from __future__ import annotations -__version__ = "0.19.2" # version line; WARNING: do not remove or change this line or comment +__version__ = "0.19.3" # version line; WARNING: do not remove or change this line or comment import collections import dataclasses From 5cf25e3459c8384feb77fcabea62f88c708f2736 Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 20 Dec 2023 10:40:25 -0600 Subject: [PATCH 2/9] changed parameter type of `Strand.set_domains` to allow `Extension`'s --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 60cf864..16aae3a 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3916,7 +3916,7 @@ def set_linear(self) -> None: """ self.set_circular(False) - def set_domains(self, domains: Iterable[Union[Domain, Loopout]]) -> None: + def set_domains(self, domains: Iterable[Union[Domain, Loopout, Extension]]) -> None: """ Sets the :any:`Domain`'s/:any:`Loopout`'s/:any:`Extension`'s of this :any:`Strand` to be `domains`, which can contain a mix of :any:`Domain`'s, :any:`Loopout`'s, and :any:`Extension`'s, From 1128beb389ea297cb5c0c6817407c28616b12c43 Mon Sep 17 00:00:00 2001 From: RayBipse Date: Wed, 20 Dec 2023 12:08:35 -0800 Subject: [PATCH 3/9] added the required build section --- readthedocs.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/readthedocs.yml b/readthedocs.yml index f8afd40..b15a595 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -22,4 +22,9 @@ python: path: . conda: - environment: environment.yml \ No newline at end of file + environment: environment.yml + +build: + os: "ubuntu-22.04" + tools: + python: "3.7" \ No newline at end of file From dcede522785e197311ed4c53facfa375ec0cd1e9 Mon Sep 17 00:00:00 2001 From: RayBipse Date: Thu, 21 Dec 2023 14:01:53 -0800 Subject: [PATCH 4/9] Removed python.version --- readthedocs.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/readthedocs.yml b/readthedocs.yml index b15a595..f266ec2 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -25,6 +25,4 @@ conda: environment: environment.yml build: - os: "ubuntu-22.04" - tools: - python: "3.7" \ No newline at end of file + os: "ubuntu-22.04" \ No newline at end of file From 3d205906717c2bf12a673671cc74786236a412ed Mon Sep 17 00:00:00 2001 From: RayBipse Date: Thu, 21 Dec 2023 14:15:20 -0800 Subject: [PATCH 5/9] Removed python.version and added back tools.python --- readthedocs.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/readthedocs.yml b/readthedocs.yml index f266ec2..f04cf7e 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -16,7 +16,6 @@ formats: all # Optionally set the version of Python and requirements required to build your docs python: - version: 3.7 install: - method: setuptools path: . @@ -25,4 +24,6 @@ conda: environment: environment.yml build: - os: "ubuntu-22.04" \ No newline at end of file + os: "ubuntu-22.04" + tools: + python: "3.7" \ No newline at end of file From 438004273b06f2314bad5579957297a83f4c73a7 Mon Sep 17 00:00:00 2001 From: RayBipse Date: Tue, 16 Jan 2024 21:42:04 -0800 Subject: [PATCH 6/9] Changed to use mamba and added python version requirement to environment.yml --- environment.yml | 1 + readthedocs.yml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 526cd10..24de4cf 100644 --- a/environment.yml +++ b/environment.yml @@ -3,4 +3,5 @@ name: scadnano-test channels: - defaults dependencies: + - python=3.7 - xlwt=1.3.0=py37_0 \ No newline at end of file diff --git a/readthedocs.yml b/readthedocs.yml index f04cf7e..93377a5 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -26,4 +26,4 @@ conda: build: os: "ubuntu-22.04" tools: - python: "3.7" \ No newline at end of file + python: "mambaforge-22.9" \ No newline at end of file From 21aa34a885bc59ec828204813a66d091e3a75c90 Mon Sep 17 00:00:00 2001 From: RayBipse Date: Tue, 16 Jan 2024 22:32:24 -0800 Subject: [PATCH 7/9] Added pip packages used to environment.yml --- environment.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 24de4cf..beb0796 100644 --- a/environment.yml +++ b/environment.yml @@ -4,4 +4,9 @@ channels: - defaults dependencies: - python=3.7 - - xlwt=1.3.0=py37_0 \ No newline at end of file + - xlwt=1.3.0=py37_0 + - pip + - pip: + - sphinx + - sphinx_rtd_theme + - openpyxl \ No newline at end of file From e5572adcc9fb355fa3baefe0997dd9549c4b2aa4 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 28 Mar 2024 09:56:40 -0700 Subject: [PATCH 8/9] fixes #297: fix oxView export exception on Loopouts --- scadnano/scadnano.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index db2c903..cb4f9f4 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -9141,8 +9141,7 @@ def _convert_design_to_oxdna_system(design: Design) -> _OxdnaSystem: elif isinstance(domain, Loopout): # we place the loopout nucleotides at temporary nonsense positions and orientations # these will be updated later, for now we just need the base - for _ in range(domain.length): - base = seq[i] + for base in seq: center = _OxdnaVector() normal = _OxdnaVector(0, -1, 0) forward = _OxdnaVector(0, 0, 1) From a220c32d338bf35f199a5ddca16950438efc98be Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 28 Mar 2024 14:40:34 -0700 Subject: [PATCH 9/9] Update scadnano.py --- scadnano/scadnano.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 433323d..3b2c531 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -7840,8 +7840,8 @@ def to_oxview_format(self, warn_duplicate_strand_names: bool = True, for d1, d2 in zip(d1range, d2range): if ((sc_strand1.dna_sequence is not None) and (sc_strand2.dna_sequence is not None) and - (sc_strand1.dna_sequence[d1] != "?") and - (sc_strand2.dna_sequence[d2] != "?") and + (sc_strand1.dna_sequence[d1] != DNA_base_wildcard) and + (sc_strand2.dna_sequence[d2] != DNA_base_wildcard) and (wc(sc_strand1.dna_sequence[d1]) != sc_strand2.dna_sequence[d2])): continue