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Package is "python-emcee" Mon Sep 20 23:32:59 2021 rev:4 rq:920080 version:3.1.1 Changes: -------- --- /work/SRC/openSUSE:Factory/python-emcee/python-emcee.changes 2021-07-03 20:51:32.516448908 +0200 +++ /work/SRC/openSUSE:Factory/.python-emcee.new.1899/python-emcee.changes 2021-09-20 23:34:35.183279812 +0200 @@ -1,0 +2,7 @@ +Sat Sep 18 19:58:41 UTC 2021 - Atri Bhattacharya <[email protected]> + +- Update to version 3.1.1: + * Added support for a progress bar description + (gh#dfm/emcee#401). + +------------------------------------------------------------------- Old: ---- emcee-3.1.0.tar.gz New: ---- emcee-3.1.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-emcee.spec ++++++ --- /var/tmp/diff_new_pack.CGUqiE/_old 2021-09-20 23:34:35.659280400 +0200 +++ /var/tmp/diff_new_pack.CGUqiE/_new 2021-09-20 23:34:35.659280400 +0200 @@ -20,7 +20,7 @@ # NEP 29: python36-numpy and -scipy are no longer available in TW %define skip_python36 1 Name: python-emcee -Version: 3.1.0 +Version: 3.1.1 Release: 0 Summary: Python affine-invariant ensemble MCMC sampling License: MIT ++++++ emcee-3.1.0.tar.gz -> emcee-3.1.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/.pre-commit-config.yaml new/emcee-3.1.1/.pre-commit-config.yaml --- old/emcee-3.1.0/.pre-commit-config.yaml 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/.pre-commit-config.yaml 2021-08-23 17:16:30.000000000 +0200 @@ -8,7 +8,7 @@ - id: debug-statements - repo: https://github.com/PyCQA/isort - rev: "5.9.1" + rev: "5.9.3" hooks: - id: isort args: [] @@ -16,11 +16,11 @@ exclude: docs/tutorials - repo: https://github.com/psf/black - rev: "21.6b0" + rev: "21.7b0" hooks: - id: black - repo: https://github.com/dfm/black_nbconvert - rev: v0.2.0 + rev: v0.3.0 hooks: - id: black_nbconvert diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/HISTORY.rst new/emcee-3.1.1/HISTORY.rst --- old/emcee-3.1.0/HISTORY.rst 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/HISTORY.rst 2021-08-23 17:16:30.000000000 +0200 @@ -1,5 +1,11 @@ .. :changelog: +3.1.1 (2021-08-23) +++++++++++++++++++ + +- Added support for a progress bar description `#401 <https://github.com/dfm/emcee/pull/401>`_ + + 3.1.0 (2021-06-25) ++++++++++++++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/PKG-INFO new/emcee-3.1.1/PKG-INFO --- old/emcee-3.1.0/PKG-INFO 2021-06-25 20:05:36.132565000 +0200 +++ new/emcee-3.1.1/PKG-INFO 2021-08-23 17:16:43.005506300 +0200 @@ -1,6 +1,6 @@ Metadata-Version: 2.1 Name: emcee -Version: 3.1.0 +Version: 3.1.1 Summary: The Python ensemble sampling toolkit for MCMC Home-page: https://emcee.readthedocs.io Author: Daniel Foreman-Mackey diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/autocorr.ipynb new/emcee-3.1.1/docs/tutorials/autocorr.ipynb --- old/emcee-3.1.0/docs/tutorials/autocorr.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/autocorr.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -30,6 +30,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20" @@ -258,7 +259,11 @@ "for n, ax in zip([10, 100, 1000], axes):\n", " nn = int(true_tau * n)\n", " ax.plot(tau / true_tau, f0, \"k\", label=\"true\")\n", - " ax.plot(tau / true_tau, autocorr_func_1d(y[0, :nn])[: window + 1], label=\"estimate\")\n", + " ax.plot(\n", + " tau / true_tau,\n", + " autocorr_func_1d(y[0, :nn])[: window + 1],\n", + " label=\"estimate\",\n", + " )\n", " ax.set_title(r\"$N = {0}\\,\\tau_\\mathrm{{true}}$\".format(n), fontsize=14)\n", " ax.set_xlabel(r\"$\\tau / \\tau_\\mathrm{true}$\")\n", "\n", @@ -307,7 +312,10 @@ " nn = int(true_tau * n)\n", " ax.plot(tau / true_tau, f0, \"k\", label=\"true\")\n", " f = np.mean(\n", - " [autocorr_func_1d(y[i, :nn], norm=False)[: window + 1] for i in range(len(y))],\n", + " [\n", + " autocorr_func_1d(y[i, :nn], norm=False)[: window + 1]\n", + " for i in range(len(y))\n", + " ],\n", " axis=0,\n", " )\n", " f /= f[0]\n", @@ -447,7 +455,9 @@ "\n", "sampler = emcee.EnsembleSampler(32, 3, log_prob)\n", "sampler.run_mcmc(\n", - " np.concatenate((np.random.randn(16, 3), 4.0 + np.random.randn(16, 3)), axis=0),\n", + " np.concatenate(\n", + " (np.random.randn(16, 3), 4.0 + np.random.randn(16, 3)), axis=0\n", + " ),\n", " 500000,\n", " progress=True,\n", ");" @@ -584,7 +594,9 @@ " # Build the GP model\n", " tau = max(1.0, init / thin)\n", " kernel = terms.RealTerm(\n", - " np.log(0.9 * np.var(z)), -np.log(tau), bounds=[(-5.0, 5.0), (-np.log(N), 0.0)]\n", + " np.log(0.9 * np.var(z)),\n", + " -np.log(tau),\n", + " bounds=[(-5.0, 5.0), (-np.log(N), 0.0)],\n", " )\n", " kernel += terms.RealTerm(\n", " np.log(0.1 * np.var(z)),\n", diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/line.ipynb new/emcee-3.1.1/docs/tutorials/line.ipynb --- old/emcee-3.1.0/docs/tutorials/line.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/line.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -30,6 +30,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20" @@ -429,7 +430,9 @@ "pos = soln.x + 1e-4 * np.random.randn(32, 3)\n", "nwalkers, ndim = pos.shape\n", "\n", - "sampler = emcee.EnsembleSampler(nwalkers, ndim, log_probability, args=(x, y, yerr))\n", + "sampler = emcee.EnsembleSampler(\n", + " nwalkers, ndim, log_probability, args=(x, y, yerr)\n", + ")\n", "sampler.run_mcmc(pos, 5000, progress=True);" ] }, diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/monitor.ipynb new/emcee-3.1.1/docs/tutorials/monitor.ipynb --- old/emcee-3.1.0/docs/tutorials/monitor.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/monitor.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -30,6 +30,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20" @@ -305,7 +306,9 @@ "source": [ "new_backend = emcee.backends.HDFBackend(filename)\n", "print(\"Initial size: {0}\".format(new_backend.iteration))\n", - "new_sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, backend=new_backend)\n", + "new_sampler = emcee.EnsembleSampler(\n", + " nwalkers, ndim, log_prob, backend=new_backend\n", + ")\n", "new_sampler.run_mcmc(None, 100)\n", "print(\"Final size: {0}\".format(new_backend.iteration))" ] @@ -345,7 +348,9 @@ "# Rinse, Wash, and Repeat as above\n", "coords = np.random.randn(32, 5)\n", "nwalkers, ndim = coords.shape\n", - "sampler2 = emcee.EnsembleSampler(nwalkers, ndim, log_prob2, backend=run2_backend)\n", + "sampler2 = emcee.EnsembleSampler(\n", + " nwalkers, ndim, log_prob2, backend=run2_backend\n", + ")\n", "\n", "# note: this is *not* necessarily the right number of iterations for this\n", "# new prior. But it will suffice to demonstrate the second backend.\n", diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/moves.ipynb new/emcee-3.1.1/docs/tutorials/moves.ipynb --- old/emcee-3.1.0/docs/tutorials/moves.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/moves.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -25,6 +25,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20" @@ -107,7 +108,11 @@ "sampler0 = emcee.EnsembleSampler(nwalkers, ndim, logprob)\n", "sampler0.run_mcmc(init, 5000)\n", "\n", - "print(\"Autocorrelation time: {0:.2f} steps\".format(sampler0.get_autocorr_time()[0]))" + "print(\n", + " \"Autocorrelation time: {0:.2f} steps\".format(\n", + " sampler0.get_autocorr_time()[0]\n", + " )\n", + ")" ] }, { @@ -201,7 +206,11 @@ ")\n", "sampler.run_mcmc(init, 5000)\n", "\n", - "print(\"Autocorrelation time: {0:.2f} steps\".format(sampler.get_autocorr_time()[0]))\n", + "print(\n", + " \"Autocorrelation time: {0:.2f} steps\".format(\n", + " sampler.get_autocorr_time()[0]\n", + " )\n", + ")\n", "\n", "plt.plot(sampler.get_chain()[:, 0, 0], \"k\", lw=0.5)\n", "plt.xlim(0, 5000)\n", diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/parallel.ipynb new/emcee-3.1.1/docs/tutorials/parallel.ipynb --- old/emcee-3.1.0/docs/tutorials/parallel.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/parallel.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -22,6 +22,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20\n", @@ -407,7 +408,9 @@ " multi_data_time = end - start\n", " print(\"Multiprocessing took {0:.1f} seconds\".format(multi_data_time))\n", " print(\n", - " \"{0:.1f} times faster(?) than serial\".format(serial_data_time / multi_data_time)\n", + " \"{0:.1f} times faster(?) than serial\".format(\n", + " serial_data_time / multi_data_time\n", + " )\n", " )" ] }, @@ -460,12 +463,16 @@ "\n", "\n", "with Pool() as pool:\n", - " sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob_data_global, pool=pool)\n", + " sampler = emcee.EnsembleSampler(\n", + " nwalkers, ndim, log_prob_data_global, pool=pool\n", + " )\n", " start = time.time()\n", " sampler.run_mcmc(initial, nsteps, progress=True)\n", " end = time.time()\n", " multi_data_global_time = end - start\n", - " print(\"Multiprocessing took {0:.1f} seconds\".format(multi_data_global_time))\n", + " print(\n", + " \"Multiprocessing took {0:.1f} seconds\".format(multi_data_global_time)\n", + " )\n", " print(\n", " \"{0:.1f} times faster than serial\".format(\n", " serial_data_time / multi_data_global_time\n", diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/tutorials/quickstart.ipynb new/emcee-3.1.1/docs/tutorials/quickstart.ipynb --- old/emcee-3.1.0/docs/tutorials/quickstart.ipynb 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/tutorials/quickstart.ipynb 2021-08-23 17:16:30.000000000 +0200 @@ -22,6 +22,7 @@ "%config InlineBackend.figure_format = \"retina\"\n", "\n", "from matplotlib import rcParams\n", + "\n", "rcParams[\"savefig.dpi\"] = 100\n", "rcParams[\"figure.dpi\"] = 100\n", "rcParams[\"font.size\"] = 20" @@ -300,7 +301,11 @@ } ], "source": [ - "print(\"Mean acceptance fraction: {0:.3f}\".format(np.mean(sampler.acceptance_fraction)))" + "print(\n", + " \"Mean acceptance fraction: {0:.3f}\".format(\n", + " np.mean(sampler.acceptance_fraction)\n", + " )\n", + ")" ] }, { diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/docs/user/blobs.rst new/emcee-3.1.1/docs/user/blobs.rst --- old/emcee-3.1.0/docs/user/blobs.rst 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/docs/user/blobs.rst 2021-08-23 17:16:30.000000000 +0200 @@ -69,10 +69,10 @@ def log_prob(params): lp = log_prior(params) if not np.isfinite(lp): - return -np.inf, -np.inf + return -np.inf, -np.inf, -np.inf ll = log_like(params) if not np.isfinite(ll): - return lp, -np.inf + return lp, -np.inf, -np.inf return lp + ll, lp, np.mean(params) coords = np.random.randn(32, 3) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/src/emcee/emcee_version.py new/emcee-3.1.1/src/emcee/emcee_version.py --- old/emcee-3.1.0/src/emcee/emcee_version.py 2021-06-25 20:05:35.000000000 +0200 +++ new/emcee-3.1.1/src/emcee/emcee_version.py 2021-08-23 17:16:42.000000000 +0200 @@ -1 +1 @@ -__version__ = "3.1.0" +__version__ = "3.1.1" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/src/emcee/ensemble.py new/emcee-3.1.1/src/emcee/ensemble.py --- old/emcee-3.1.0/src/emcee/ensemble.py 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/src/emcee/ensemble.py 2021-08-23 17:16:30.000000000 +0200 @@ -261,6 +261,7 @@ thin=None, store=True, progress=False, + progress_kwargs=None, ): """Advance the chain as a generator @@ -287,6 +288,8 @@ ``'notebook'``, which shows a progress bar suitable for Jupyter notebooks. If ``False``, no progress bar will be shown. + progress_kwargs (Optional[dict]): A ``dict`` of keyword arguments + to be passed to the tqdm call. skip_initial_state_check (Optional[bool]): If ``True``, a check that the initial_state can fully explore the space will be skipped. (default: ``False``) @@ -383,10 +386,12 @@ model = Model( self.log_prob_fn, self.compute_log_prob, map_fn, self._random ) + if progress_kwargs is None: + progress_kwargs = {} # Inject the progress bar total = None if iterations is None else iterations * yield_step - with get_progress_bar(progress, total) as pbar: + with get_progress_bar(progress, total, **progress_kwargs) as pbar: i = 0 for _ in count() if iterations is None else range(iterations): for _ in range(yield_step): diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/src/emcee/pbar.py new/emcee-3.1.1/src/emcee/pbar.py --- old/emcee-3.1.0/src/emcee/pbar.py 2021-06-25 20:05:13.000000000 +0200 +++ new/emcee-3.1.1/src/emcee/pbar.py 2021-08-23 17:16:30.000000000 +0200 @@ -28,7 +28,7 @@ pass -def get_progress_bar(display, total): +def get_progress_bar(display, total, **kwargs): """Get a progress bar interface with given properties If the tqdm library is not installed, this will always return a "progress @@ -38,6 +38,7 @@ display (bool or str): Should the bar actually show the progress? Or a string to indicate which tqdm bar to use. total (int): The total size of the progress bar. + kwargs (dict): Optional keyword arguments to be passed to the tqdm call. """ if display: @@ -49,8 +50,8 @@ return _NoOpPBar() else: if display is True: - return tqdm.tqdm(total=total) + return tqdm.tqdm(total=total, **kwargs) else: - return getattr(tqdm, "tqdm_" + display)(total=total) + return getattr(tqdm, "tqdm_" + display)(total=total, **kwargs) return _NoOpPBar() diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/emcee-3.1.0/src/emcee.egg-info/PKG-INFO new/emcee-3.1.1/src/emcee.egg-info/PKG-INFO --- old/emcee-3.1.0/src/emcee.egg-info/PKG-INFO 2021-06-25 20:05:35.000000000 +0200 +++ new/emcee-3.1.1/src/emcee.egg-info/PKG-INFO 2021-08-23 17:16:42.000000000 +0200 @@ -1,6 +1,6 @@ Metadata-Version: 2.1 Name: emcee -Version: 3.1.0 +Version: 3.1.1 Summary: The Python ensemble sampling toolkit for MCMC Home-page: https://emcee.readthedocs.io Author: Daniel Foreman-Mackey
